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Sample records for automated multistep genetic

  1. Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic

    PubMed Central

    Shukla, Chinmay A

    2017-01-01

    The implementation of automation in the multistep flow synthesis is essential for transforming laboratory-scale chemistry into a reliable industrial process. In this review, we briefly introduce the role of automation based on its application in synthesis viz. auto sampling and inline monitoring, optimization and process control. Subsequently, we have critically reviewed a few multistep flow synthesis and suggested a possible control strategy to be implemented so that it helps to reliably transfer the laboratory-scale synthesis strategy to a pilot scale at its optimum conditions. Due to the vast literature in multistep synthesis, we have classified the literature and have identified the case studies based on few criteria viz. type of reaction, heating methods, processes involving in-line separation units, telescopic synthesis, processes involving in-line quenching and process with the smallest time scale of operation. This classification will cover the broader range in the multistep synthesis literature. PMID:28684977

  2. An Automated, Multi-Step Monte Carlo Burnup Code System.

    SciTech Connect

    TRELLUE, HOLLY R.

    2003-07-14

    Version 02 MONTEBURNS Version 2 calculates coupled neutronic/isotopic results for nuclear systems and produces a large number of criticality and burnup results based on various material feed/removal specifications, power(s), and time intervals. MONTEBURNS is a fully automated tool that links the LANL MCNP Monte Carlo transport code with a radioactive decay and burnup code. Highlights on changes to Version 2 are listed in the transmittal letter. Along with other minor improvements in MONTEBURNS Version 2, the option was added to use CINDER90 instead of ORIGEN2 as the depletion/decay part of the system. CINDER90 is a multi-group depletion code developed at LANL and is not currently available from RSICC. This MONTEBURNS release was tested with various combinations of CCC-715/MCNPX 2.4.0, CCC-710/MCNP5, CCC-700/MCNP4C, CCC-371/ORIGEN2.2, ORIGEN2.1 and CINDER90. Perl is required software and is not included in this distribution. MCNP, ORIGEN2, and CINDER90 are not included.

  3. Design of a new automated multi-step outflow test apparatus

    NASA Astrophysics Data System (ADS)

    Figueras, J.; Gribb, M. M.; McNamara, J. P.

    2006-12-01

    Modeling flow and transport in the vadose zone requires knowledge of the soil hydraulic properties. Laboratories studies involving vadose zone soils typically include use of the multistep outflow method (MSO), which can provide information about wetting and drying soil-moisture and hydraulic conductivity curves from a single test. However, manual MSO testing is time consuming and measurement errors can be easily introduced. A computer-automated system has been designed to allow convenient measurement of soil-water characteristic curves. Computer-controlled solenoid valves are used to regulate the pressure inside Tempe cells to drain soil samples, and outflow volumes are measured with a pressure transducer. The electronic components of the system are controlled using LabVIEW software. This system has been optimized for undisturbed core samples. System performance has been evaluated by comparing results from undisturbed samples subjected first to manual MSO testing and then automated testing. The automated and manual MSO tests yielded similar drying soil-water characteristic curves. These curves are further compared to in-situ measurements and those obtained using pedotransfer functions for a semi-arid watershed.

  4. Genetic circuit design automation.

    PubMed

    Nielsen, Alec A K; Der, Bryan S; Shin, Jonghyeon; Vaidyanathan, Prashant; Paralanov, Vanya; Strychalski, Elizabeth A; Ross, David; Densmore, Douglas; Voigt, Christopher A

    2016-04-01

    Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits forEscherichia coli(880,000 base pairs of DNA), for which each DNA sequence was built as predicted by the software with no additional tuning. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts), and across all circuits 92% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decision-making, control, sensing, or spatial organization. Copyright © 2016, American Association for the Advancement of Science.

  5. Automated multi-step purification protocol for Angiotensin-I-Converting-Enzyme (ACE).

    PubMed

    Eisele, Thomas; Stressler, Timo; Kranz, Bertolt; Fischer, Lutz

    2012-12-12

    Highly purified proteins are essential for the investigation of the functional and biochemical properties of proteins. The purification of a protein requires several steps, which are often time-consuming. In our study, the Angiotensin-I-Converting-Enzyme (ACE; EC 3.4.15.1) was solubilised from pig lung without additional detergents, which are commonly used, under mild alkaline conditions in a Tris-HCl buffer (50mM, pH 9.0) for 48h. An automation of the ACE purification was performed using a multi-step protocol in less than 8h, resulting in a purified protein with a specific activity of 37Umg(-1) (purification factor 308) and a yield of 23.6%. The automated ACE purification used an ordinary fast-protein-liquid-chromatography (FPLC) system equipped with two additional switching valves. These switching valves were needed for the buffer stream inversion and for the connection of the Superloop™ used for the protein parking. Automated ACE purification was performed using four combined chromatography steps, including two desalting procedures. The purification methods contained two hydrophobic interaction chromatography steps, a Cibacron 3FG-A chromatography step and a strong anion exchange chromatography step. The purified ACE was characterised by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and native-PAGE. The estimated monomer size of the purified glycosylated ACE was determined to be ∼175kDa by SDS-PAGE, with the dimeric form at ∼330kDa as characterised by a native PAGE using a novel activity staining protocol. For the activity staining, the tripeptide l-Phe-Gly-Gly was used as the substrate. The ACE cleaved the dipeptide Gly-Gly, releasing the l-Phe to be oxidised with l-amino acid oxidase. Combined with peroxidase and o-dianisidine, the generated H(2)O(2) stained a brown coloured band. This automated purification protocol can be easily adapted to be used with other protein purification tasks. Copyright © 2012 Elsevier B.V. All rights

  6. A miniature integrated device for automated multistep genetic assays

    PubMed Central

    Anderson, Rolfe C.; Su, Xing; Bogdan, Gregory J.; Fenton, Jeffery

    2000-01-01

    A highly integrated monolithic device was developed that automatically carries out a complex series of molecular processes on multiple samples. The device is capable of extracting and concentrating nucleic acids from milliliter aqueous samples and performing microliter chemical amplification, serial enzymatic reactions, metering, mixing and nucleic acid hybridization. The device, which is smaller than a credit card, can manipulate over 10 reagents in more than 60 sequential operations and was tested for the detection of mutations in a 1.6 kb region of the HIV genome from serum samples containing as few as 500 copies of the RNA. The elements in this device are readily linked into complex, flexible and highly parallel analysis networks for high throughput sample preparation or, conversely, for low cost portable DNA analysis instruments in point-of-care medical diagnostics, environmental testing and defensive biological agent detection. PMID:10871383

  7. Automating multi-step paper-based assays using integrated layering of reagents.

    PubMed

    Jahanshahi-Anbuhi, Sana; Kannan, Balamurali; Pennings, Kevin; Monsur Ali, M; Leung, Vincent; Giang, Karen; Wang, Jingyun; White, Dawn; Li, Yingfu; Pelton, Robert H; Brennan, John D; Filipe, Carlos D M

    2017-02-28

    We describe a versatile and simple method to perform sequential reactions on paper analytical devices by stacking dry pullulan films on paper, where each film contains one or more reagents or acts as a delay layer. Exposing the films to an aqueous solution of the analyte leads to sequential dissolution of the films in a temporally controlled manner followed by diffusive mixing of the reagents, so that sequential reactions can be performed. The films can be easily arranged for lateral flow assays or for spot tests (reactions take place sequentially in the z-direction). We have tested the general feasibility of the approach using three different model systems to demonstrate different capabilities: 1) pH ramping from low to high and high to low to demonstrate timing control; 2) rapid ready-to-use two-step Simon's assays on paper for detection of drugs of abuse utilizing a 2-layer stack containing two different reagents to demonstrate the ability to perform assays in the z-direction; and 3) sequential cell lysing and colorimetric detection of an intracellular bacterial enzyme, to demonstrate the ability of the method to perform sample preparation and analysis in the form of a spot assay. Overall, these studies demonstrate the potential of stacked pullulan films as useful components to enable multi-step assays on simple paper-based devices.

  8. Multi-step excitation energy transfer engineered in genetic fusions of natural and synthetic light-harvesting proteins.

    PubMed

    Mancini, Joshua A; Kodali, Goutham; Jiang, Jianbing; Reddy, Kanumuri Ramesh; Lindsey, Jonathan S; Bryant, Donald A; Dutton, P Leslie; Moser, Christopher C

    2017-02-01

    Synthetic proteins designed and constructed from first principles with minimal reference to the sequence of any natural protein have proven robust and extraordinarily adaptable for engineering a range of functions. Here for the first time we describe the expression and genetic fusion of a natural photosynthetic light-harvesting subunit with a synthetic protein designed for light energy capture and multi-step transfer. We demonstrate excitation energy transfer from the bilin of the CpcA subunit (phycocyanin α subunit) of the cyanobacterial photosynthetic light-harvesting phycobilisome to synthetic four-helix-bundle proteins accommodating sites that specifically bind a variety of selected photoactive tetrapyrroles positioned to enhance energy transfer by relay. The examination of combinations of different bilin, chlorin and bacteriochlorin cofactors has led to identification of the preconditions for directing energy from the bilin light-harvesting antenna into synthetic protein-cofactor constructs that can be customized for light-activated chemistry in the cell.

  9. Layout Optimization Method for Magnetic Circuit using Multi-step Utilization of Genetic Algorithm Combined with Design Space Reduction

    NASA Astrophysics Data System (ADS)

    Okamoto, Yoshifumi; Tominaga, Yusuke; Sato, Shuji

    The layout optimization with the ON-OFF information of magnetic material in finite elements is one of the most attractive tools in initial conceptual and practical design of electrical machinery for engineers. The heuristic algorithms based on the random search allow the engineers to define the general-purpose objects, however, there are many iterations of finite element analysis, and it is difficult to realize the practical solution without island and void distribution by using direct search method, for example, simulated annealing (SA), genetic algorithm (GA), and so on. This paper presents the layout optimization method based on GA. Proposed method can arrive at the practical solution by means of multi-step utilization of GA, and the convergence speed is considerably improved by using the combination with the reduction process of design space.

  10. Genetic model of multi-step breast carcinogenesis involving the epithelium and stroma: clues to tumour-microenvironment interactions.

    PubMed

    Kurose, K; Hoshaw-Woodard, S; Adeyinka, A; Lemeshow, S; Watson, P H; Eng, C

    2001-09-01

    Although numerous studies have reported that high frequencies of loss of heterozygosity (LOH) at various chromosomal arms have been identified in breast cancer, differential LOH in the neoplastic epithelial and surrounding stromal compartments has not been well examined. Using laser capture microdissection, which enables separation of neoplastic epithelium from surrounding stroma, we microdissected each compartment of 41 sporadic invasive adenocarcinomas of the breast. Frequent LOH was identified in both neoplastic epithelial and/or stromal compartments, ranging from 25 to 69% in the neoplastic epithelial cells, and from 17 to 61% in the surrounding stromal cells, respectively. The great majority of markers showed a higher frequency of LOH in the neoplastic epithelial compartment than in the stroma, suggesting that LOH in neoplastic epithelial cells might precede LOH in surrounding stromal cells. Furthermore, we sought to examine pair-wise associations of particular genetic alterations in either epithelial or stromal compartments. Seventeen pairs of markers showed statistically significant associations. We also propose a genetic model of multi-step carcinogenesis for the breast involving the epithelial and stromal compartments and note that genetic alterations occur in the epithelial compartments as the earlier steps followed by LOH in the stromal compartments. Our study strongly suggests that interactions between breast epithelial and stromal compartments might play a critical role in breast carcinogenesis and several genetic alterations in both epithelial and stromal compartments are required for breast tumour growth and progression.

  11. Programming cells: towards an automated 'Genetic Compiler'.

    PubMed

    Clancy, Kevin; Voigt, Christopher A

    2010-08-01

    One of the visions of synthetic biology is to be able to program cells using a language that is similar to that used to program computers or robotics. For large genetic programs, keeping track of the DNA on the level of nucleotides becomes tedious and error prone, requiring a new generation of computer-aided design (CAD) software. To push the size of projects, it is important to abstract the designer from the process of part selection and optimization. The vision is to specify genetic programs in a higher-level language, which a genetic compiler could automatically convert into a DNA sequence. Steps towards this goal include: defining the semantics of the higher-level language, algorithms to select and assemble parts, and biophysical methods to link DNA sequence to function. These will be coupled to graphic design interfaces and simulation packages to aid in the prediction of program dynamics, optimize genes, and scan projects for errors.

  12. Automated discrete element method calibration using genetic and optimization algorithms

    NASA Astrophysics Data System (ADS)

    Do, Huy Q.; Aragón, Alejandro M.; Schott, Dingena L.

    2017-06-01

    This research aims at developing a universal methodology for automated calibration of microscopic properties of modelled granular materials. The proposed calibrator can be applied for different experimental set-ups. Two optimization approaches: (1) a genetic algorithm and (2) DIRECT optimization, are used to identify discrete element method input model parameters, e.g., coefficients of sliding and rolling friction. The algorithms are used to minimize the objective function characterized by the discrepancy between the experimental macroscopic properties and the associated numerical results. Two test cases highlight the robustness, stability, and reliability of the two algorithms used for automated discrete element method calibration with different set-ups.

  13. Automated computer vision interpretation for physical and genetic mapping experiments

    SciTech Connect

    Pathak, D.K.; Perlin, M.W.

    1994-09-01

    Much of the high-throughput data currently generated in the molecular genetics laboratory is in the form of two dimensional images. In physical mapping, a high-density gridded filter containing thousands YACs or cosmids can be hybridized against a single labeled probe, such as the IRS-PCR products of a radiation hybrid (RH). In genetic mapping, hundreds of polymorphic dinucleotide repeat PCR experiments can be multiplexed into distinct lanes, size ranges, and fluorescent colors on a single run of an Applied Biosystems (ABl) 373A automated DNA sequencer. For all its advantages such high-throughput data introduces a new fundamental bottleneck: the greatly increased time, expense, and error of scoring these assays when relying solely on the human visual system. Toward this end, we have developed a novel computer vision automation architecture that addresses the needs of high-throughput data interpretation in the molecular genetics laboratory. A flexible knowledge-based approach is used to systematically detect and analyze signal features, motivated by how human experts perform the interpretation. This architecture enables customization to similar hybridization-and gel-based tasks. Our prototype system has thus far been tested on both hybridization data and ABl gel images.

  14. AutoBioCAD: full biodesign automation of genetic circuits.

    PubMed

    Rodrigo, Guillermo; Jaramillo, Alfonso

    2013-05-17

    Synthetic regulatory networks with prescribed functions are engineered by assembling a reduced set of functional elements. We could also assemble them computationally if the mathematical models of those functional elements were predictive enough in different genetic contexts. Only after achieving this will we have libraries of models of biological parts able to provide predictive dynamical behaviors for most circuits constructed with them. We thus need tools that can automatically explore different genetic contexts, in addition to being able to use such libraries to design novel circuits with targeted dynamics. We have implemented a new tool, AutoBioCAD, aimed at the automated design of gene regulatory circuits. AutoBioCAD loads a library of models of genetic elements and implements evolutionary design strategies to produce (i) nucleotide sequences encoding circuits with targeted dynamics that can then be tested experimentally and (ii) circuit models for testing regulation principles in natural systems, providing a new tool for synthetic biology. AutoBioCAD can be used to model and design genetic circuits with dynamic behavior, thanks to the incorporation of stochastic effects, robustness, qualitative dynamics, multiobjective optimization, or degenerate nucleotide sequences, all facilitating the link with biological part/circuit engineering.

  15. MALDI-TOF MS analysis of soluble PEG based multi-step synthetic reaction mixtures with automated detection of reaction failure.

    PubMed

    Enjalbal, Christine; Ribière, Patrice; Lamaty, Frédéric; Yadav-Bhatnagar, Neerja; Martinez, Jean; Aubagnac, Jean-Louis

    2005-05-01

    Macromolecules of tunable solubility, used to mimic inert insoluble materials while maintaining solution conditions, allowed the performance of efficient supported organic chemistry and facilitated in situ reaction monitoring. To satisfy the high throughput requirements of automated synthetic processes, organic syntheses carried out on bifunctional polyethylene glycol polymers (PEG(3400)-OH) were monitored step-by-step by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). A protocol was designed to control the ionization mechanism of such polymers exhibiting high affinity for alkali metal cations. Automated, rapid, and reliable data interpretation was performed by an in-house developed visual basic application relying on the sodiated ion accurate monoisotopic mass measurement. The methodology was illustrated through the monitoring of a six-step synthetic scheme.

  16. A Parallel Genetic Algorithm for Automated Electronic Circuit Design

    NASA Technical Reports Server (NTRS)

    Long, Jason D.; Colombano, Silvano P.; Haith, Gary L.; Stassinopoulos, Dimitris

    2000-01-01

    Parallelized versions of genetic algorithms (GAs) are popular primarily for three reasons: the GA is an inherently parallel algorithm, typical GA applications are very compute intensive, and powerful computing platforms, especially Beowulf-style computing clusters, are becoming more affordable and easier to implement. In addition, the low communication bandwidth required allows the use of inexpensive networking hardware such as standard office ethernet. In this paper we describe a parallel GA and its use in automated high-level circuit design. Genetic algorithms are a type of trial-and-error search technique that are guided by principles of Darwinian evolution. Just as the genetic material of two living organisms can intermix to produce offspring that are better adapted to their environment, GAs expose genetic material, frequently strings of 1s and Os, to the forces of artificial evolution: selection, mutation, recombination, etc. GAs start with a pool of randomly-generated candidate solutions which are then tested and scored with respect to their utility. Solutions are then bred by probabilistically selecting high quality parents and recombining their genetic representations to produce offspring solutions. Offspring are typically subjected to a small amount of random mutation. After a pool of offspring is produced, this process iterates until a satisfactory solution is found or an iteration limit is reached. Genetic algorithms have been applied to a wide variety of problems in many fields, including chemistry, biology, and many engineering disciplines. There are many styles of parallelism used in implementing parallel GAs. One such method is called the master-slave or processor farm approach. In this technique, slave nodes are used solely to compute fitness evaluations (the most time consuming part). The master processor collects fitness scores from the nodes and performs the genetic operators (selection, reproduction, variation, etc.). Because of dependency

  17. First Experience with Clinical-Grade [18F]FPP (RGD)2: An Automated Multi-step Radiosynthesis for Clinical PET Studies

    PubMed Central

    Chin, Frederick T.; Shen, Bin; Liu, Shuanglong; Berganos, Rhona A.; Chang, Edwin; Mittra, Erik; Chen, Xiaoyuan; Gambhir, Sanjiv S.

    2013-01-01

    Purpose A reliable and routine process to introduce a new 18F-labeled dimeric RGD-peptide tracer ([18F]FPP(RGD)2) for noninvasive imaging of αvβ3 expression in tumors needed to be developed so the tracer could be evaluated for the first time in man. Clinical-grade [18F]FPP (RGD)2 was screened in mouse prior to our first pilot study in human. Procedures [18F]FPP(RGD)2 was synthesized by coupling 4-nitrophenyl-2-[18F]fluoropropionate ([18F]NPE) with the dimeric RGD-peptide (PEG3-c(RGDyK)2). Imaging studies with [18F]FPP (RGD)2 in normal mice and a healthy human volunteer were carried out using small animal and clinical PET scanners, respectively. Results Through optimization of each radiosynthetic step, [18F]FPP(RGD)2 was obtained with RCYs of 16.9±2.7% (n=8, EOB) and specific radioactivity of 114±72 GBq/μmol (3.08±1.95 Ci/μmol; n=8, EOB) after 170 min of radiosynthesis. In our mouse studies, high radioactivity uptake was only observed in the kidneys and bladder with the clinical-grade tracer. Favorable [18F]FPP (RGD)2 biodistribution in human studies, with low background signal in the head, neck, and thorax, showed the potential applications of this RGD-peptide tracer for detecting and monitoring tumor growth and metastasis. Conclusions A reliable, routine, and automated radiosynthesis of clinical-grade [18F]FPP(RGD)2 was established. PET imaging in a healthy human volunteer illustrates that [18F]FPP(RGD)2 possesses desirable pharmacokinetic properties for clinical noninvasive imaging of αvβ3 expression. Further imaging studies using [18F]FPP(RGD)2 in patient volunteers are now under active investigation. PMID:21400112

  18. First experience with clinical-grade ([18F]FPP(RGD₂): an automated multi-step radiosynthesis for clinical PET studies.

    PubMed

    Chin, Frederick T; Shen, Bin; Liu, Shuanglong; Berganos, Rhona A; Chang, Edwin; Mittra, Erik; Chen, Xiaoyuan; Gambhir, Sanjiv S

    2012-02-01

    A reliable and routine process to introduce a new ¹⁸F-labeled dimeric RGD-peptide tracer ([¹⁸F]FPP(RGD₂) for noninvasive imaging of α(v)β₃ expression in tumors needed to be developed so the tracer could be evaluated for the first time in man. Clinical-grade [¹⁸F]FPP(RGD)₂ was screened in mouse prior to our first pilot study in human. [¹⁸F]FPP(RGD)₂ was synthesized by coupling 4-nitrophenyl-2-[¹⁸F]fluoropropionate ([¹⁸F]NPE) with the dimeric RGD-peptide (PEG₃-c(RGDyK)₂). Imaging studies with [¹⁸F]FPP(RGD)₂ in normal mice and a healthy human volunteer were carried out using small animal and clinical PET scanners, respectively. Through optimization of each radiosynthetic step, [¹⁸F]FPP(RGD)₂ was obtained with RCYs of 16.9 ± 2.7% (n = 8, EOB) and specific radioactivity of 114 ± 72 GBq/μmol (3.08 ± 1.95 Ci/μmol; n = 8, EOB) after 170 min of radiosynthesis. In our mouse studies, high radioactivity uptake was only observed in the kidneys and bladder with the clinical-grade tracer. Favorable [¹⁸F]FPP(RGD)₂ biodistribution in human studies, with low background signal in the head, neck, and thorax, showed the potential applications of this RGD-peptide tracer for detecting and monitoring tumor growth and metastasis. A reliable, routine, and automated radiosynthesis of clinical-grade [¹⁸F]FPP(RGD)₂ was established. PET imaging in a healthy human volunteer illustrates that [¹⁸F]FPP(RGD)₂ possesses desirable pharmacokinetic properties for clinical noninvasive imaging of α(v)β₃ expression. Further imaging studies using [¹⁸F]FPP(RGD)₂ in patient volunteers are now under active investigation.

  19. Automating the packing heuristic design process with genetic programming.

    PubMed

    Burke, Edmund K; Hyde, Matthew R; Kendall, Graham; Woodward, John

    2012-01-01

    The literature shows that one-, two-, and three-dimensional bin packing and knapsack packing are difficult problems in operational research. Many techniques, including exact, heuristic, and metaheuristic approaches, have been investigated to solve these problems and it is often not clear which method to use when presented with a new instance. This paper presents an approach which is motivated by the goal of building computer systems which can design heuristic methods. The overall aim is to explore the possibilities for automating the heuristic design process. We present a genetic programming system to automatically generate a good quality heuristic for each instance. It is not necessary to change the methodology depending on the problem type (one-, two-, or three-dimensional knapsack and bin packing problems), and it therefore has a level of generality unmatched by other systems in the literature. We carry out an extensive suite of experiments and compare with the best human designed heuristics in the literature. Note that our heuristic design methodology uses the same parameters for all the experiments. The contribution of this paper is to present a more general packing methodology than those currently available, and to show that, by using this methodology, it is possible for a computer system to design heuristics which are competitive with the human designed heuristics from the literature. This represents the first packing algorithm in the literature able to claim human competitive results in such a wide variety of packing domains.

  20. Directed multistep biocatalysis using tailored permeabilized cells.

    PubMed

    Krauser, Steffen; Weyler, Christian; Blaß, Lisa Katharina; Heinzle, Elmar

    2013-01-01

    : Recent developments in the field of biocatalysis using permeabilized cells are reviewed here, with a special emphasis on the newly emerging area of multistep biocatalysis using permeabilized cells. New methods of metabolic engineering using in silico network design and new methods of genetic engineering provide the opportunity to design more complex biocatalysts for the synthesis of complex biomolecules. Methods for the permeabilization of cells are thoroughly reviewed. We provide an extended review of useful available databases and bioinformatics tools, particularly for setting up genome-scale reconstructed networks. Examples described include phosphorylated carbohydrates, sugar nucleotides, and polyketides.

  1. Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis.

    PubMed

    Besse, P; Taylor, G; Carroll, B; Berding, N; Burner, D; McIntyre, C L

    1998-10-01

    An assessment of genetic diversity within and between Saccharum, Old World Erianthus sect. Ripidium, and North American E.giganteus (S.giganteum) was conducted using Amplified Fragment Length Polymorphism (AFLP(TM)) markers. An automated gel scoring system (GelCompar(TM)) was successfully used to analyse the complex AFLP patterns obtained in sugarcane and its relatives. Similarity coefficient calculations and clustering revealed a genetic structure for Saccharum and Erianthus sect. Ripidium that was identical to the one previously obtained using other molecular marker types, showing the appropriateness of AFLP markers and the associated automated analysis in assessing genetic diversity in sugarcane. A genetic structure that correlated with cytotype (2n=30, 60, 90) was revealed within the North American species, E. giganteus (S.giganteum). Complex relationships among Saccharum, Erianthus sect. Ripidium, and North American E.giganteus were revealed and are discussed in the light of a similar study which involved RAPD markers.

  2. Genetic Influences on Cognitive Function Using the Cambridge Neuropsychological Test Automated Battery

    ERIC Educational Resources Information Center

    Singer, Jamie J.; MacGregor, Alex J.; Cherkas, Lynn F.; Spector, Tim D.

    2006-01-01

    The genetic relationship between intelligence and components of cognition remains controversial. Conflicting results may be a function of the limited number of methods used in experimental evaluation. The current study is the first to use CANTAB (The Cambridge Neuropsychological Test Automated Battery). This is a battery of validated computerised…

  3. Automated Test Assembly for Cognitive Diagnosis Models Using a Genetic Algorithm

    ERIC Educational Resources Information Center

    Finkelman, Matthew; Kim, Wonsuk; Roussos, Louis A.

    2009-01-01

    Much recent psychometric literature has focused on cognitive diagnosis models (CDMs), a promising class of instruments used to measure the strengths and weaknesses of examinees. This article introduces a genetic algorithm to perform automated test assembly alongside CDMs. The algorithm is flexible in that it can be applied whether the goal is to…

  4. Automated Test Assembly for Cognitive Diagnosis Models Using a Genetic Algorithm

    ERIC Educational Resources Information Center

    Finkelman, Matthew; Kim, Wonsuk; Roussos, Louis A.

    2009-01-01

    Much recent psychometric literature has focused on cognitive diagnosis models (CDMs), a promising class of instruments used to measure the strengths and weaknesses of examinees. This article introduces a genetic algorithm to perform automated test assembly alongside CDMs. The algorithm is flexible in that it can be applied whether the goal is to…

  5. A Droplet Microfluidic Platform for Automating Genetic Engineering.

    PubMed

    Gach, Philip C; Shih, Steve C C; Sustarich, Jess; Keasling, Jay D; Hillson, Nathan J; Adams, Paul D; Singh, Anup K

    2016-05-20

    We present a water-in-oil droplet microfluidic platform for transformation, culture and expression of recombinant proteins in multiple host organisms including bacteria, yeast and fungi. The platform consists of a hybrid digital microfluidic/channel-based droplet chip with integrated temperature control to allow complete automation and integration of plasmid addition, heat-shock transformation, addition of selection medium, culture, and protein expression. The microfluidic format permitted significant reduction in consumption (100-fold) of expensive reagents such as DNA and enzymes compared to the benchtop method. The chip contains a channel to continuously replenish oil to the culture chamber to provide a fresh supply of oxygen to the cells for long-term (∼5 days) cell culture. The flow channel also replenished oil lost to evaporation and increased the number of droplets that could be processed and cultured. The platform was validated by transforming several plasmids into Escherichia coli including plasmids containing genes for fluorescent proteins GFP, BFP and RFP; plasmids with selectable markers for ampicillin or kanamycin resistance; and a Golden Gate DNA assembly reaction. We also demonstrate the applicability of this platform for transformation in widely used eukaryotic organisms such as Saccharomyces cerevisiae and Aspergillus niger. Duration and temperatures of the microfluidic heat-shock procedures were optimized to yield transformation efficiencies comparable to those obtained by benchtop methods with a throughput up to 6 droplets/min. The proposed platform offers potential for automation of molecular biology experiments significantly reducing cost, time and variability while improving throughput.

  6. Genetic design automation: engineering fantasy or scientific renewal?

    PubMed

    Lux, Matthew W; Bramlett, Brian W; Ball, David A; Peccoud, Jean

    2012-02-01

    The aim of synthetic biology is to make genetic systems more amenable to engineering, which has naturally led to the development of computer-aided design (CAD) tools. Experimentalists still primarily rely on project-specific ad hoc workflows instead of domain-specific tools, which suggests that CAD tools are lagging behind the front line of the field. Here, we discuss the scientific hurdles that have limited the productivity gains anticipated from existing tools. We argue that the real value of efforts to develop CAD tools is the formalization of genetic design rules that determine the complex relationships between genotype and phenotype.

  7. Applying flow chemistry: methods, materials, and multistep synthesis.

    PubMed

    McQuade, D Tyler; Seeberger, Peter H

    2013-07-05

    The synthesis of complex molecules requires control over both chemical reactivity and reaction conditions. While reactivity drives the majority of chemical discovery, advances in reaction condition control have accelerated method development/discovery. Recent tools include automated synthesizers and flow reactors. In this Synopsis, we describe how flow reactors have enabled chemical advances in our groups in the areas of single-stage reactions, materials synthesis, and multistep reactions. In each section, we detail the lessons learned and propose future directions.

  8. A Parallel Genetic Algorithm for Automated Electronic Circuit Design

    NASA Technical Reports Server (NTRS)

    Lohn, Jason D.; Colombano, Silvano P.; Haith, Gary L.; Stassinopoulos, Dimitris; Norvig, Peter (Technical Monitor)

    2000-01-01

    We describe a parallel genetic algorithm (GA) that automatically generates circuit designs using evolutionary search. A circuit-construction programming language is introduced and we show how evolution can generate practical analog circuit designs. Our system allows circuit size (number of devices), circuit topology, and device values to be evolved. We present experimental results as applied to analog filter and amplifier design tasks.

  9. Complex Genetics of Behavior: BXDs in the Automated Home-Cage.

    PubMed

    Loos, Maarten; Verhage, Matthijs; Spijker, Sabine; Smit, August B

    2017-01-01

    This chapter describes a use case for the genetic dissection and automated analysis of complex behavioral traits using the genetically diverse panel of BXD mouse recombinant inbred strains. Strains of the BXD resource differ widely in terms of gene and protein expression in the brain, as well as in their behavioral repertoire. A large mouse resource opens the possibility for gene finding studies underlying distinct behavioral phenotypes, however, such a resource poses a challenge in behavioral phenotyping. To address the specifics of large-scale screening we describe how to investigate: (1) how to assess mouse behavior systematically in addressing a large genetic cohort, (2) how to dissect automation-derived longitudinal mouse behavior into quantitative parameters, and (3) how to map these quantitative traits to the genome, deriving loci underlying aspects of behavior.

  10. Using digital electronic design flow to create a Genetic Design Automation tool.

    PubMed

    Gendrault, Y; Madec, M; Wlotzko, V; Andraud, M; Lallement, C; Haiech, J

    2012-01-01

    Synthetic bio-systems become increasingly more complex and their development is lengthy and expensive. In the same way, in microelectronics, the design process of very complex circuits has benefited from many years of experience. It is now partly automated through Electronic Design Automation tools. Both areas present analogies that can be used to create a Genetic Design Automation tool inspired from EDA tools used in digital electronics. This tool would allow moving away from a totally manual design of bio-systems to assisted conception. This ambitious project is presented in this paper, with a deep focus on the tool that automatically generates models of bio-systems directly usable in electronic simulators.

  11. Automated identification of pathways from quantitative genetic interaction data

    PubMed Central

    Battle, Alexis; Jonikas, Martin C; Walter, Peter; Weissman, Jonathan S; Koller, Daphne

    2010-01-01

    High-throughput quantitative genetic interaction (GI) measurements provide detailed information regarding the structure of the underlying biological pathways by reporting on functional dependencies between genes. However, the analytical tools for fully exploiting such information lag behind the ability to collect these data. We present a novel Bayesian learning method that uses quantitative phenotypes of double knockout organisms to automatically reconstruct detailed pathway structures. We applied our method to a recent data set that measures GIs for endoplasmic reticulum (ER) genes, using the unfolded protein response as a quantitative phenotype. The results provided reconstructions of known functional pathways including N-linked glycosylation and ER-associated protein degradation. It also contained novel relationships, such as the placement of SGT2 in the tail-anchored biogenesis pathway, a finding that we experimentally validated. Our approach should be readily applicable to the next generation of quantitative GI data sets, as assays become available for additional phenotypes and eventually higher-level organisms. PMID:20531408

  12. Deadlock-free genetic scheduling algorithm for automated manufacturing systems based on deadlock control policy.

    PubMed

    Xing, KeYi; Han, LiBin; Zhou, MengChu; Wang, Feng

    2012-06-01

    Deadlock-free control and scheduling are vital for optimizing the performance of automated manufacturing systems (AMSs) with shared resources and route flexibility. Based on the Petri net models of AMSs, this paper embeds the optimal deadlock avoidance policy into the genetic algorithm and develops a novel deadlock-free genetic scheduling algorithm for AMSs. A possible solution of the scheduling problem is coded as a chromosome representation that is a permutation with repetition of parts. By using the one-step look-ahead method in the optimal deadlock control policy, the feasibility of a chromosome is checked, and infeasible chromosomes are amended into feasible ones, which can be easily decoded into a feasible deadlock-free schedule. The chromosome representation and polynomial complexity of checking and amending procedures together support the cooperative aspect of genetic search for scheduling problems strongly.

  13. Automated DNA extraction from genetically modified maize using aminosilane-modified bacterial magnetic particles.

    PubMed

    Ota, Hiroyuki; Lim, Tae-Kyu; Tanaka, Tsuyoshi; Yoshino, Tomoko; Harada, Manabu; Matsunaga, Tadashi

    2006-09-18

    A novel, automated system, PNE-1080, equipped with eight automated pestle units and a spectrophotometer was developed for genomic DNA extraction from maize using aminosilane-modified bacterial magnetic particles (BMPs). The use of aminosilane-modified BMPs allowed highly accurate DNA recovery. The (A(260)-A(320)):(A(280)-A(320)) ratio of the extracted DNA was 1.9+/-0.1. The DNA quality was sufficiently pure for PCR analysis. The PNE-1080 offered rapid assay completion (30 min) with high accuracy. Furthermore, the results of real-time PCR confirmed that our proposed method permitted the accurate determination of genetically modified DNA composition and correlated well with results obtained by conventional cetyltrimethylammonium bromide (CTAB)-based methods.

  14. Single-Cell Genetic Analysis Using Automated Microfluidics to Resolve Somatic Mosaicism.

    PubMed

    Szulwach, Keith E; Chen, Peilin; Wang, Xiaohui; Wang, Jing; Weaver, Lesley S; Gonzales, Michael L; Sun, Gang; Unger, Marc A; Ramakrishnan, Ramesh

    2015-01-01

    Somatic mosaicism occurs throughout normal development and contributes to numerous disease etiologies, including tumorigenesis and neurological disorders. Intratumor genetic heterogeneity is inherent to many cancers, creating challenges for effective treatments. Unfortunately, analysis of bulk DNA masks subclonal phylogenetic architectures created by the acquisition and distribution of somatic mutations amongst cells. As a result, single-cell genetic analysis is becoming recognized as vital for accurately characterizing cancers. Despite this, methods for single-cell genetics are lacking. Here we present an automated microfluidic workflow enabling efficient cell capture, lysis, and whole genome amplification (WGA). We find that ~90% of the genome is accessible in single cells with improved uniformity relative to current single-cell WGA methods. Allelic dropout (ADO) rates were limited to 13.75% and variant false discovery rates (SNV FDR) were 4.11x10(-6), on average. Application to ER-/PR-/HER2+ breast cancer cells and matched normal controls identified novel mutations that arose in a subpopulation of cells and effectively resolved the segregation of known cancer-related mutations with single-cell resolution. Finally, we demonstrate effective cell classification using mutation profiles with 10X average exome coverage depth per cell. Our data demonstrate an efficient automated microfluidic platform for single-cell WGA that enables the resolution of somatic mutation patterns in single cells.

  15. Influence of parameter settings in automated scoring of AFLPs on population genetic analysis.

    PubMed

    Herrmann, Marc; Holderegger, Rolf; Van Strien, Maarten J

    2013-01-01

    The use of procedures for the automated scoring of amplified fragment length polymorphisms (AFLP) fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package rawgeno to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations (F(st)). Steps were implemented in r to automatically run the scoring process in rawgeno for a set of different parameter combinations. While we found the scoring parameters minimum bin width and minimum number of samples per bin to have only weak influence on pairwise F(st) values, maximum bin width and bin reproducibility had much stronger effects. The minimum average bin fluorescence scoring parameter affected F(st) values in an only moderate way. At a range of scoring parameters around the default settings of rawgeno, the number of polymorphic bins as well as pairwise F(st) values stayed rather constant. This study thus shows the particularities of AFLP scoring, be it either manual or automatical, can have profound effects on subsequent population genetic analysis.

  16. Optimal open multistep discretization formulas for real-time simulation

    NASA Technical Reports Server (NTRS)

    Moerder, Daniel D.; Calise, Anthony J.; Clemmons, Paul

    1993-01-01

    The performance of digital real-time simulations is considered. A figure of merit is derived that quantifies a simulation's fidelity in terms of the time-domain discrepancy between its output and that of the plant it simulates, assuming that the plant is linearizable and asymptotically stable. This performance index is then used in deriving an easily automated procedure for calculating optimal values for free parameters in plant discretizations based on a generalized form of open linear multistep integration formulas. The theory is demonstrated in simulating the rigid-body dynamics of a fully articulated helicopter rotor blade system.

  17. On stiffly stable implicit linear multistep methods.

    NASA Technical Reports Server (NTRS)

    Cooke, C. H.

    1972-01-01

    The motivation to increase the step size with no degradation of numerical accuracy and stability has led to the discovery of particular members of the class of stiffly stable implicit linear multistep algorithms. Sufficient conditions for a consistent linear multistep method to be stiffly stable are given. These conditions involve properties of the stability mapping from the extended complex plane onto itself.

  18. Multistep synthesis of a radiolabeled imaging probe using integrated microfluidics.

    PubMed

    Lee, Chung-Cheng; Sui, Guodong; Elizarov, Arkadij; Shu, Chengyi Jenny; Shin, Young-Shik; Dooley, Alek N; Huang, Jiang; Daridon, Antoine; Wyatt, Paul; Stout, David; Kolb, Hartmuth C; Witte, Owen N; Satyamurthy, Nagichettiar; Heath, James R; Phelps, Michael E; Quake, Stephen R; Tseng, Hsian-Rong

    2005-12-16

    Microreactor technology has shown potential for optimizing synthetic efficiency, particularly in preparing sensitive compounds. We achieved the synthesis of an [(18)F]fluoride-radiolabeled molecular imaging probe, 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG), in an integrated microfluidic device. Five sequential processes-[18F]fluoride concentration, water evaporation, radiofluorination, solvent exchange, and hydrolytic deprotection-proceeded with high radio-chemical yield and purity and with shorter synthesis time relative to conventional automated synthesis. Multiple doses of [18F]FDG for positron emission tomography imaging studies in mice were prepared. These results, which constitute a proof of principle for automated multistep syntheses at the nanogram to microgram scale, could be generalized to a range of radiolabeled substrates.

  19. Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra.

    PubMed

    Meiler, Jens; Will, Martin

    2002-03-06

    The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using 13C NMR spectrum as readily obtainable information. By means of artificial neural networks a fast and accurate method for calculating the 13C NMR spectrum of the generated structures exists. The method is implemented and tested successfully for organic molecules with up to 18 non-hydrogen atoms.

  20. Simplifying multiobjective optimization: An automated design methodology for the nondominated sorted genetic algorithm-II

    NASA Astrophysics Data System (ADS)

    Reed, Patrick; Minsker, Barbara S.; Goldberg, David E.

    2003-07-01

    Many water resources problems require careful balancing of fiscal, technical, and social objectives. Informed negotiation and balancing of objectives can be greatly aided through the use of evolutionary multiobjective optimization (EMO) algorithms, which can evolve entire tradeoff (or Pareto) surfaces within a single run. The primary difficulty in using these methods lies in the large number of parameters that must be specified to ensure that these algorithms effectively quantify design tradeoffs. This technical note addresses this difficulty by introducing a multipopulation design methodology that automates parameter specification for the nondominated sorted genetic algorithm-II (NSGA-II). The NSGA-II design methodology is successfully demonstrated on a multiobjective long-term groundwater monitoring application. Using this methodology, multiobjective optimization problems can now be solved automatically with only a few simple user inputs.

  1. Automated, quantitative cognitive/behavioral screening of mice: for genetics, pharmacology, animal cognition and undergraduate instruction.

    PubMed

    Gallistel, C R; Balci, Fuat; Freestone, David; Kheifets, Aaron; King, Adam

    2014-02-26

    We describe a high-throughput, high-volume, fully automated, live-in 24/7 behavioral testing system for assessing the effects of genetic and pharmacological manipulations on basic mechanisms of cognition and learning in mice. A standard polypropylene mouse housing tub is connected through an acrylic tube to a standard commercial mouse test box. The test box has 3 hoppers, 2 of which are connected to pellet feeders. All are internally illuminable with an LED and monitored for head entries by infrared (IR) beams. Mice live in the environment, which eliminates handling during screening. They obtain their food during two or more daily feeding periods by performing in operant (instrumental) and Pavlovian (classical) protocols, for which we have written protocol-control software and quasi-real-time data analysis and graphing software. The data analysis and graphing routines are written in a MATLAB-based language created to simplify greatly the analysis of large time-stamped behavioral and physiological event records and to preserve a full data trail from raw data through all intermediate analyses to the published graphs and statistics within a single data structure. The data-analysis code harvests the data several times a day and subjects it to statistical and graphical analyses, which are automatically stored in the "cloud" and on in-lab computers. Thus, the progress of individual mice is visualized and quantified daily. The data-analysis code talks to the protocol-control code, permitting the automated advance from protocol to protocol of individual subjects. The behavioral protocols implemented are matching, autoshaping, timed hopper-switching, risk assessment in timed hopper-switching, impulsivity measurement, and the circadian anticipation of food availability. Open-source protocol-control and data-analysis code makes the addition of new protocols simple. Eight test environments fit in a 48 in x 24 in x 78 in cabinet; two such cabinets (16 environments) may be

  2. Automatic time-motion study of a multistep preoperative process.

    PubMed

    Meyer, Mark A; Seim, Andreas R; Fairbrother, Pamela; Egan, Marie T; Sandberg, Warren S

    2008-06-01

    Hospitals use time-motion studies to monitor process effectiveness and patient waiting. Manual tracking is labor-intensive and potentially influences system performance. New technology known as indoor positioning systems (IPS) may allow automatic monitoring of patient waiting and progress. The authors tested whether an IPS can track patients through a multistep preoperative process. The authors used an IPS between October 14, 2005, and June 13, 2006, to track patients in a multistep ambulatory preoperative process: needle localization and excisional biopsy of a breast lesion. The process was distributed across the ambulatory surgery and radiology departments of a large academic hospital. Direct observation of the process was used to develop a workflow template. The authors then developed software to convert the IPS data into usable time-motion data suitable for monitoring process efficiency over time. The authors assigned tags to 306 patients during the study period. Eighty patients never underwent the procedure or never had their tag affixed. One hundred seventy-seven (78%) of the remaining 226 patients successfully matched the workflow template. Process time stamps were automatically extracted from the successful matches, measuring time before radiology (mean +/- SD, 77 +/- 35 min), time in radiology (105 +/- 35 min), and time between radiology and operating room (80 +/- 60 min), which summed to total preoperative time (261 +/- 67 min). The authors have demonstrated that it is possible to use a combination of IPS technology and sequence alignment pattern matching software to automate the time-motion study of patients in a multidepartment, multistep process with the only day-of-surgery intervention being the application of a tag when the patient arrives.

  3. Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies.

    PubMed

    Atkinson, Jonathan A; Lobet, Guillaume; Noll, Manuel; Meyer, Patrick E; Griffiths, Marcus; Wells, Darren M

    2017-10-01

    Genetic analyses of plant root systems require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between automated tools (that are prone to error and extract only a limited number of architectural traits) or semi-automated ones (that are highly time consuming). We trained a Random Forest algorithm to infer architectural traits from automatically extracted image descriptors. The training was performed on a subset of the dataset, then applied to its entirety. This strategy allowed us to (i) decrease the image analysis time by 73% and (ii) extract meaningful architectural traits based on image descriptors. We also show that these traits are sufficient to identify the quantitative trait loci that had previously been discovered using a semi-automated method. We have shown that combining semi-automated image analysis with machine learning algorithms has the power to increase the throughput of large-scale root studies. We expect that such an approach will enable the quantification of more complex root systems for genetic studies. We also believe that our approach could be extended to other areas of plant phenotyping. © The Authors 2017. Published by Oxford University Press.

  4. Modelling molecule-surface interactions--an automated quantum-classical approach using a genetic algorithm.

    PubMed

    Herbers, Claudia R; Johnston, Karen; van der Vegt, Nico F A

    2011-06-14

    We present an automated and efficient method to develop force fields for molecule-surface interactions. A genetic algorithm (GA) is used to parameterise a classical force field so that the classical adsorption energy landscape of a molecule on a surface matches the corresponding landscape from density functional theory (DFT) calculations. The procedure performs a sophisticated search in the parameter phase space and converges very quickly. The method is capable of fitting a significant number of structures and corresponding adsorption energies. Water on a ZnO(0001) surface was chosen as a benchmark system but the method is implemented in a flexible way and can be applied to any system of interest. In the present case, pairwise Lennard Jones (LJ) and Coulomb potentials are used to describe the molecule-surface interactions. In the course of the fitting procedure, the LJ parameters are refined in order to reproduce the adsorption energy landscape. The classical model is capable of describing a wide range of energies, which is essential for a realistic description of a fluid-solid interface.

  5. Development of an automated fluorescence microscopy system for photomanipulation of genetically encoded photoactivatable proteins (optogenetics) in live cells.

    PubMed

    Araki, Nobukazu; Ikeda, Yuka; Kato, Takuma; Kawai, Katsuhisa; Egami, Youhei; Miyake, Katsuya; Tsurumaki, Nobuhide; Yamaguchi, Mitsunari

    2014-06-01

    Photomanipulation of genetically encoded light-sensitive protein activity, also known as optogenetics, is one of the most innovative recent microscopy techniques in the fields of cell biology and neurobiology. Although photomanipulation is usually performed by diverting the photobleaching mode of a confocal laser microscope, photobleaching by the laser scanning unit is not always suitable for photoactivation. We have developed a simple automated wide-field fluorescence microscopy system for the photomanipulation of genetically encoded photoactivatable proteins in live cells. An electrically automated fluorescence microscope can be controlled through MetaMorph imaging software, making it possible to acquire time-lapse, multiwavelength images of live cells. Using the journal (macro recording) function of MetaMorph, we wrote a macro program to change the excitation filter for photoactivation and illumination area during the intervals of image acquisition. When this program was run on the wide-field fluorescence microscope, cells expressing genetically encoded photoactivatable Rac1, which is activated under blue light, showed morphological changes such as lamellipodial extension and cell surface ruffling in the illuminated region. Using software-based development, we successfully constructed a fully automated photoactivation microscopy system for a mercury lamp-based fluorescence microscope. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Automated synthesis of both the topology and numerical parameters for seven patented optical lens systems using genetic programming

    NASA Astrophysics Data System (ADS)

    Jones, Lee W.; Al-Sakran, Sameer H.; Koza, John R.

    2005-08-01

    This paper describes how genetic programming was used as an automated invention machine to synthesize both the topology and numerical parameters for seven previously patented optical lens systems, including one aspherical system and one issued in the 21st-century. Two of the evolved optical lens systems infringe the claims of the patents and the others are novel solutions that satisfy the design goals stated in the patent. The automatic synthesis was done "from scratch"--that is, without starting from a pre-existing good design and without pre-specifying the number of lenses, the topological layout of the lenses, or the numerical parameters of the lenses. Genetic programming is a form of evolutionary computation used to automatically solve problems. It starts from a high-level statement of what needs to be done and progressively breeds a population of candidate individuals over many generations using the principle of Darwinian natural selection and genetic recombination. The paper describes how genetic programming created eyepieces that duplicated the functionality of seven previously patented lens systems. The seven designs were created in a substantially similar and routine way, suggesting that the use of genetic programming in the automated design of both the topology and numerical parameters for optical lens systems may have widespread utility.

  7. Multistep Methods for Integrating the Solar System

    DTIC Science & Technology

    1988-07-01

    Technical Report 1055 [Multistep Methods for Integrating the Solar System 0 Panayotis A. Skordos’ MIT Artificial Intelligence Laboratory DTIC S D g8...RMA ELEENT. PROECT. TASK Artific ial Inteligence Laboratory ARE1A G WORK UNIT NUMBERS 545 Technology Square Cambridge, MA 02139 IL. CONTROLLING...describes research done at the Artificial Intelligence Laboratory of the Massachusetts Institute of Technology, supported by the Advanced Research Projects

  8. Linear Multistep Methods for Integrating Reversible Differential Equations

    NASA Astrophysics Data System (ADS)

    Evans, N. Wyn; Tremaine, Scott

    1999-10-01

    This paper studies multistep methods for the integration of reversible dynamical systems, with particular emphasis on the planar Kepler problem. It has previously been shown by Cano & Sanz-Serna that reversible linear multisteps for first-order differential equations are generally unstable. Here we report on a subset of these methods-the zero-growth methods-that evade these instabilities. We provide an algorithm for identifying these rare methods. We find and study all zero-growth, reversible multisteps with six or fewer steps. This select group includes two well-known second-order multisteps (the trapezoidal and explicit midpoint methods), as well as three new fourth-order multisteps-one of which is explicit. Variable time steps can be readily implemented without spoiling the reversibility. Tests on Keplerian orbits show that these new reversible multisteps work well on orbits with low or moderate eccentricity, although at least 100 steps per radian are required for stability.

  9. The stability problem for linear multistep methods

    NASA Astrophysics Data System (ADS)

    Aceto, L.; Trigiante, D.

    2007-12-01

    The paper reviews results on rigorous proofs for stability properties of classes of linear multistep methods (LMMs) used either as IVMs or as BVMs. The considered classes are not only the well-known classical ones (BDF, Adams, ...) along with their BVM correspondent, but also those which were considered unstable as IVMs, but stable as BVMs. Among the latter we find two classes which deserve attention because of their peculiarity: the TOMs (top order methods) which have the highest order allowed to a LMM and the Bs-LMMs which have the property to carry with each method its natural continuous extension.

  10. Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles

    PubMed Central

    2013-01-01

    Background Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) that associate with clinical phenotypes, but these SNPs usually explain just a small part of the heritability and have relatively modest effect sizes. In contrast, SNPs that associate with metabolite levels generally explain a higher percentage of the genetic variation and demonstrate larger effect sizes. Still, the discovery of SNPs associated with metabolite levels is challenging since testing all metabolites measured in typical metabolomics studies with all SNPs comes with a severe multiple testing penalty. We have developed an automated workflow approach that utilizes prior knowledge of biochemical pathways present in databases like KEGG and BioCyc to generate a smaller SNP set relevant to the metabolite. This paper explores the opportunities and challenges in the analysis of GWAS of metabolomic phenotypes and provides novel insights into the genetic basis of metabolic variation through the re-analysis of published GWAS datasets. Results Re-analysis of the published GWAS dataset from Illig et al. (Nature Genetics, 2010) using a pathway-based workflow (http://www.myexperiment.org/packs/319.html), confirmed previously identified hits and identified a new locus of human metabolic individuality, associating Aldehyde dehydrogenase family1 L1 (ALDH1L1) with serine/glycine ratios in blood. Replication in an independent GWAS dataset of phospholipids (Demirkan et al., PLoS Genetics, 2012) identified two novel loci supported by additional literature evidence: GPAM (Glycerol-3 phosphate acyltransferase) and CBS (Cystathionine beta-synthase). In addition, the workflow approach provided novel insight into the affected pathways and relevance of some of these gene-metabolite pairs in disease development and progression. Conclusions We demonstrate the utility of automated exploitation of background knowledge present in pathway databases for the analysis of GWAS

  11. Multistep sintering to synthesize fast lithium garnets

    NASA Astrophysics Data System (ADS)

    Xu, Biyi; Duan, Huanan; Xia, Wenhao; Guo, Yiping; Kang, Hongmei; Li, Hua; Liu, Hezhou

    2016-01-01

    A multistep sintering schedule is developed to synthesize Li7La3Zr2O12 (LLZO) doped with 0.2 mol% Al3+. The effect of sintering steps on phase, relative density and ionic conductivity of Al-doped LLZO has been evaluated using powder X-Ray diffraction (XRD), scanning electron microscopy (SEM), 27Al magic spinning nuclear magnetic resonance (NMR) spectroscopy and electrochemical impedance spectroscopy (EIS). The results show that by holding the sample at 900 °C for 6 h, the mixture of tetragonal and cubic garnet phases are obtained; by continuously holding at 1100 °C for 6 h, the tetragonal phase completely transforms into cubic phase; by holding at 1200 °C, the relative density increases without decomposition of the cubic phase. The Al-LLZO pellets after multistep sintering exhibit cubic phase, relative density of 94.25% and ionic conductivity of 4.5 × 10-4 S cm-1 at room temperature. Based on the observation, a sintering model is proposed and discussed.

  12. Synthesis of Silver Nanostructures by Multistep Methods

    PubMed Central

    Zhang, Tong; Song, Yuan-Jun; Zhang, Xiao-Yang; Wu, Jing-Yuan

    2014-01-01

    The shape of plasmonic nanostructures such as silver and gold is vital to their physical and chemical properties and potential applications. Recently, preparation of complex nanostructures with rich function by chemical multistep methods is the hotspot of research. In this review we introduce three typical multistep methods to prepare silver nanostructures with well-controlled shapes, including the double reductant method, etching technique and construction of core-shell nanostructures. The growth mechanism of double the reductant method is that different favorable facets of silver nanocrystals are produced in different reductants, which can be used to prepare complex nanostructures such as nanoflags with ultranarrow resonant band bandwidth or some silver nanostructures which are difficult to prepare using other methods. The etching technique can selectively remove nanoparticles to achieve the aim of shape control and is widely used for the synthesis of nanoflowers and hollow nanostructures. Construction of core-shell nanostructures is another tool to control shape and size. The three methods can not only prepare various silver nanostructures with well-controlled shapes, which exhibit unique optical properties, such as strong surface-enhanced Raman scattering (SERS) signal and localized surface plasmon resonance (LSPR) effect, but also have potential application in many areas. PMID:24670722

  13. Differential genetic regulation of motor activity and anxiety-related behaviors in mice using an automated home cage task.

    PubMed

    Kas, Martien J H; de Mooij-van Malsen, Annetrude J G; Olivier, Berend; Spruijt, Berry M; van Ree, Jan M

    2008-08-01

    Traditional behavioral tests, such as the open field test, measure an animal's responsiveness to a novel environment. However, it is generally difficult to assess whether the behavioral response obtained from these tests relates to the expression level of motor activity and/or to avoidance of anxiogenic areas. Here, an automated home cage environment for mice was designed to obtain independent measures of motor activity levels and of sheltered feeding preference during three consecutive days. Chronic treatment with the anxiolytic drug chlordiazepoxide (5 and 10 mg/kg/day) in C57BL/6J mice reduced sheltered feeding preference without altering motor activity levels. Furthermore, two distinct chromosome substitution strains, derived from C57BL/6J (host strain) and A/J (donor strain) inbred strains, expressed either increased sheltering preference in females (chromosome 15) or reduced motor activity levels in females and males (chromosome 1) when compared to C57BL/6J. Longitudinal behavioral monitoring revealed that these phenotypic differences maintained after adaptation to the home cage. Thus, by using new automated behavioral phenotyping approaches, behavior can be dissociated into distinct behavioral domains (e.g., anxiety-related and motor activity domains) with different underlying genetic origin and pharmacological responsiveness.

  14. An automated diagnosis system of liver disease using artificial immune and genetic algorithms.

    PubMed

    Liang, Chunlin; Peng, Lingxi

    2013-04-01

    The rise of health care cost is one of the world's most important problems. Disease prediction is also a vibrant research area. Researchers have approached this problem using various techniques such as support vector machine, artificial neural network, etc. This study typically exploits the immune system's characteristics of learning and memory to solve the problem of liver disease diagnosis. The proposed system applies a combination of two methods of artificial immune and genetic algorithm to diagnose the liver disease. The system architecture is based on artificial immune system. The learning procedure of system adopts genetic algorithm to interfere the evolution of antibody population. The experiments use two benchmark datasets in our study, which are acquired from the famous UCI machine learning repository. The obtained diagnosis accuracies are very promising with regard to the other diagnosis system in the literatures. These results suggest that this system may be a useful automatic diagnosis tool for liver disease.

  15. Spi-1/PU.1 transgenic mice develop multistep erythroleukemias.

    PubMed Central

    Moreau-Gachelin, F; Wendling, F; Molina, T; Denis, N; Titeux, M; Grimber, G; Briand, P; Vainchenker, W; Tavitian, A

    1996-01-01

    Insertional mutagenesis of the spi-1 gene is associated with the emergence of malignant proerythroblasts during Friend virus-induced acute erythroleukemia. To determine the role of spi-1/PU.1 in the genesis of leukemia, we generated spi-1 transgenic mice. In one founder line the transgene was overexpressed as an unexpected-size transcript in various mouse tissues. Homozygous transgenic animals gave rise to live-born offspring, but 50% of the animals developed a multistep erythroleukemia within 1.5 to 6 months of birth whereas the remainder survived without evidence of disease. At the onset of the disease, mice became severely anemic. Their hematopoietic tissues were massively invaded with nontumorigenic proerythroblasts that express a high level of Spi-1 protein. These transgenic proerythroblasts are partially blocked in differentiation and strictly dependent on erythropoietin for their proliferation both in vivo and in vitro. A complete but transient regression of the disease was observed after erythrocyte transfusion, suggesting that the constitutive expression of spi-1 is related to the block of the differentiation of erythroid precursors. At relapse, erythropoietin-independent malignant proerythroblasts arose. Growth factor autonomy could be partially explained by the autocrine secretion of erythropoietin; however, other genetic events appear to be necessary to confer the full malignant phenotype. These results reveal that overexpression of spi-1 is essential for malignant erythropoiesis and does not alter other hematopoietic lineages. PMID:8628313

  16. Automated microscopy system for detection and genetic characterization of fetal nucleated red blood cells on slides

    NASA Astrophysics Data System (ADS)

    Ravkin, Ilya; Temov, Vladimir

    1998-04-01

    The detection and genetic analysis of fetal cells in maternal blood will permit noninvasive prenatal screening for genetic defects. Applied Imaging has developed and is currently evaluating a system for semiautomatic detection of fetal nucleated red blood cells on slides and acquisition of their DNA probe FISH images. The specimens are blood smears from pregnant women (9 - 16 weeks gestation) enriched for nucleated red blood cells (NRBC). The cells are identified by using labeled monoclonal antibodies directed to different types of hemoglobin chains (gamma, epsilon); the nuclei are stained with DAPI. The Applied Imaging system has been implemented with both Olympus BX and Nikon Eclipse series microscopes which were equipped with transmission and fluorescence optics. The system includes the following motorized components: stage, focus, transmission, and fluorescence filter wheels. A video camera with light integration (COHU 4910) permits low light imaging. The software capabilities include scanning, relocation, autofocusing, feature extraction, facilities for operator review, and data analysis. Detection of fetal NRBCs is achieved by employing a combination of brightfield and fluorescence images of nuclear and cytoplasmic markers. The brightfield and fluorescence images are all obtained with a single multi-bandpass dichroic mirror. A Z-stack of DNA probe FISH images is acquired by moving focus and switching excitation filters. This stack is combined to produce an enhanced image for presentation and spot counting.

  17. Automated detection of lung nodules in CT images using shape-based genetic algorithm.

    PubMed

    Dehmeshki, Jamshid; Ye, Xujiong; Lin, Xinyu; Valdivieso, Manlio; Amin, Hamdan

    2007-09-01

    A shape-based genetic algorithm template-matching (GATM) method is proposed for the detection of nodules with spherical elements. A spherical-oriented convolution-based filtering scheme is used as a pre-processing step for enhancement. To define the fitness function for GATM, a 3D geometric shape feature is calculated at each voxel and then combined into a global nodule intensity distribution. Lung nodule phantom images are used as reference images for template matching. The proposed method has been validated on a clinical dataset of 70 thoracic CT scans (involving 16,800 CT slices) that contains 178 nodules as a gold standard. A total of 160 nodules were correctly detected by the proposed method and resulted in a detection rate of about 90%, with the number of false positives at approximately 14.6/scan (0.06/slice). The high-detection performance of the method suggested promising potential for clinical applications.

  18. Development of a Genetic Algorithm to Automate Clustering of a Dependency Structure Matrix

    NASA Technical Reports Server (NTRS)

    Rogers, James L.; Korte, John J.; Bilardo, Vincent J.

    2006-01-01

    Much technology assessment and organization design data exists in Microsoft Excel spreadsheets. Tools are needed to put this data into a form that can be used by design managers to make design decisions. One need is to cluster data that is highly coupled. Tools such as the Dependency Structure Matrix (DSM) and a Genetic Algorithm (GA) can be of great benefit. However, no tool currently combines the DSM and a GA to solve the clustering problem. This paper describes a new software tool that interfaces a GA written as an Excel macro with a DSM in spreadsheet format. The results of several test cases are included to demonstrate how well this new tool works.

  19. A taste of individualized medicine: physicians’ reactions to automated genetic interpretations

    PubMed Central

    Lærum, Hallvard; Bremer, Sara; Bergan, Stein; Grünfeld, Thomas

    2014-01-01

    The potential of pharmacogenomics is well documented, and functionality exploiting this knowledge is about to be introduced into electronic medical records. To explore physicians’ reactions to automatic interpretations of genetic tests, we built a prototype with a simple interpretive algorithm. The algorithm was adapted to the needs of physicians handling immunosuppressive treatment during organ transplantation. Nine physicians were observed expressing their thoughts while using the prototype for two patient scenarios. The computer screen and audio were recorded, and the qualitative results triangulated with responses to a survey instrument. The physicians’ reactions to the prototype were very positive; they clearly trusted the results and the theory behind them. The explanation of the algorithm was prominently placed in the user interface for transparency, although this design led to considerable confusion. Background information and references should be available, but considerably less prominent than the result and recommendation. PMID:24001515

  20. Multistep, effective drug distribution within solid tumors

    PubMed Central

    Shemi, Amotz; Khvalevsky, Elina Zorde; Gabai, Rachel Malka; Domb, Abraham; Barenholz, Yechezkel

    2015-01-01

    The distribution of drugs within solid tumors presents a long-standing barrier for efficient cancer therapies. Tumors are highly resistant to diffusion, and the lack of blood and lymphatic flows suppresses convection. Prolonged, continuous intratumoral drug delivery from a miniature drug source offers an alternative to both systemic delivery and intratumoral injection. Presented here is a model of drug distribution from such a source, in a multistep process. At delivery onset the drug mainly affects the closest surroundings. Such ‘priming’ enables drug penetration to successive cell layers. Tumor ‘void volume’ (volume not occupied by cells) increases, facilitating lymphatic perfusion. The drug is then transported by hydraulic convection downstream along interstitial fluid pressure (IFP) gradients, away from the tumor core. After a week tumor cell death occurs throughout the entire tumor and IFP gradients are flattened. Then, the drug is transported mainly by ‘mixing’, powered by physiological bulk body movements. Steady state is achieved and the drug covers the entire tumor over several months. Supporting measurements are provided from the LODER™ system, releasing siRNA against mutated KRAS over months in pancreatic cancer in-vivo models. LODER™ was also successfully employed in a recent Phase 1/2 clinical trial with pancreatic cancer patients. PMID:26416413

  1. Genetic algorithm based feature selection combined with dual classification for the automated detection of proliferative diabetic retinopathy.

    PubMed

    Welikala, R A; Fraz, M M; Dehmeshki, J; Hoppe, A; Tah, V; Mann, S; Williamson, T H; Barman, S A

    2015-07-01

    Proliferative diabetic retinopathy (PDR) is a condition that carries a high risk of severe visual impairment. The hallmark of PDR is the growth of abnormal new vessels. In this paper, an automated method for the detection of new vessels from retinal images is presented. This method is based on a dual classification approach. Two vessel segmentation approaches are applied to create two separate binary vessel map which each hold vital information. Local morphology features are measured from each binary vessel map to produce two separate 4-D feature vectors. Independent classification is performed for each feature vector using a support vector machine (SVM) classifier. The system then combines these individual outcomes to produce a final decision. This is followed by the creation of additional features to generate 21-D feature vectors, which feed into a genetic algorithm based feature selection approach with the objective of finding feature subsets that improve the performance of the classification. Sensitivity and specificity results using a dataset of 60 images are 0.9138 and 0.9600, respectively, on a per patch basis and 1.000 and 0.975, respectively, on a per image basis.

  2. A generalized theory of chromatography and multistep liquid extraction

    NASA Astrophysics Data System (ADS)

    Chizhkov, V. P.; Boitsov, V. N.

    2017-03-01

    A generalized theory of chromatography and multistep liquid extraction is developed. The principles of highly efficient processes for fine preparative separation of binary mixture components on a fixed sorbent layer are discussed.

  3. Automated Lead Optimization of MMP-12 Inhibitors Using a Genetic Algorithm.

    PubMed

    Pickett, Stephen D; Green, Darren V S; Hunt, David L; Pardoe, David A; Hughes, Ian

    2011-01-13

    Traditional lead optimization projects involve long synthesis and testing cycles, favoring extensive structure-activity relationship (SAR) analysis and molecular design steps, in an attempt to limit the number of cycles that a project must run to optimize a development candidate. Microfluidic-based chemistry and biology platforms, with cycle times of minutes rather than weeks, lend themselves to unattended autonomous operation. The bottleneck in the lead optimization process is therefore shifted from synthesis or test to SAR analysis and design. As such, the way is open to an algorithm-directed process, without the need for detailed user data analysis. Here, we present results of two synthesis and screening experiments, undertaken using traditional methodology, to validate a genetic algorithm optimization process for future application to a microfluidic system. The algorithm has several novel features that are important for the intended application. For example, it is robust to missing data and can suggest compounds for retest to ensure reliability of optimization. The algorithm is first validated on a retrospective analysis of an in-house library embedded in a larger virtual array of presumed inactive compounds. In a second, prospective experiment with MMP-12 as the target protein, 140 compounds are submitted for synthesis over 10 cycles of optimization. Comparison is made to the results from the full combinatorial library that was synthesized manually and tested independently. The results show that compounds selected by the algorithm are heavily biased toward the more active regions of the library, while the algorithm is robust to both missing data (compounds where synthesis failed) and inactive compounds. This publication places the full combinatorial library and biological data into the public domain with the intention of advancing research into algorithm-directed lead optimization methods.

  4. Genetic Algorithm Based Framework for Automation of Stochastic Modeling of Multi-Season Streamflows

    NASA Astrophysics Data System (ADS)

    Srivastav, R. K.; Srinivasan, K.; Sudheer, K.

    2009-05-01

    bootstrap (MABB) ) based on the explicit objective functions of minimizing the relative bias and relative root mean square error in estimating the storage capacity of the reservoir. The optimal parameter set of the hybrid model is obtained based on the search over a multi- dimensional parameter space (involving simultaneous exploration of the parametric (PAR(1)) as well as the non-parametric (MABB) components). This is achieved using the efficient evolutionary search based optimization tool namely, non-dominated sorting genetic algorithm - II (NSGA-II). This approach helps in reducing the drudgery involved in the process of manual selection of the hybrid model, in addition to predicting the basic summary statistics dependence structure, marginal distribution and water-use characteristics accurately. The proposed optimization framework is used to model the multi-season streamflows of River Beaver and River Weber of USA. In case of both the rivers, the proposed GA-based hybrid model yields a much better prediction of the storage capacity (where simultaneous exploration of both parametric and non-parametric components is done) when compared with the MLE-based hybrid models (where the hybrid model selection is done in two stages, thus probably resulting in a sub-optimal model). This framework can be further extended to include different linear/non-linear hybrid stochastic models at other temporal and spatial scales as well.

  5. Automated extraction of DNA from blood and PCR setup using a Tecan Freedom EVO liquid handler for forensic genetic STR typing of reference samples.

    PubMed

    Stangegaard, Michael; Frøslev, Tobias G; Frank-Hansen, Rune; Hansen, Anders J; Morling, Niels

    2011-04-01

    We have implemented and validated automated protocols for DNA extraction and PCR setup using a Tecan Freedom EVO liquid handler mounted with the Te-MagS magnetic separation device (Tecan, Männedorf, Switzerland). The protocols were validated for accredited forensic genetic work according to ISO 17025 using the Qiagen MagAttract DNA Mini M48 kit (Qiagen GmbH, Hilden, Germany) from fresh whole blood and blood from deceased individuals. The workflow was simplified by returning the DNA extracts to the original tubes minimizing the risk of misplacing samples. The tubes that originally contained the samples were washed with MilliQ water before the return of the DNA extracts. The PCR was setup in 96-well microtiter plates. The methods were validated for the kits: AmpFℓSTR Identifiler, SGM Plus and Yfiler (Applied Biosystems, Foster City, CA), GenePrint FFFL and PowerPlex Y (Promega, Madison, WI). The automated protocols allowed for extraction and addition of PCR master mix of 96 samples within 3.5h. In conclusion, we demonstrated that (1) DNA extraction with magnetic beads and (2) PCR setup for accredited, forensic genetic short tandem repeat typing can be implemented on a simple automated liquid handler leading to the reduction of manual work, and increased quality and throughput.

  6. Multi-step motion planning: Application to free-climbing robots

    NASA Astrophysics Data System (ADS)

    Bretl, Timothy Wolfe

    This dissertation addresses the problem of planning the motion of a multi-limbed robot to "free-climb" vertical rock surfaces. Free-climbing relies on natural features and friction (such as holes or protrusions) rather than special fixtures or tools. It requires strength, but more importantly it requires deliberate reasoning: not only must the robot decide how to adjust its posture to reach the next feature without falling, it must plan an entire sequence of steps, where each one might have future consequences. This process of reasoning is called multi-step planning. A multi-step planning framework is presented for computing non-gaited, free-climbing motions. This framework derives from an analysis of a free-climbing robot's configuration space, which can be decomposed into constraint manifolds associated with each state of contact between the robot and its environment. An understanding of the adjacency between manifolds motivates a two-stage strategy that uses a candidate sequence of steps to direct the subsequent search for motions. Three algorithms are developed to support the framework. The first algorithm reduces the amount of time required to plan each potential step, a large number of which must be considered over an entire multi-step search. It extends the probabilistic roadmap (PRM) approach based on an analysis of the interaction between balance and the topology of closed kinematic chains. The second algorithm addresses a problem with the PRM approach, that it is unable to distinguish challenging steps (which may be critical) from impossible ones. This algorithm detects impossible steps explicitly, using automated algebraic inference and machine learning. The third algorithm provides a fast constraint checker (on which the PRM approach depends), in particular a test of balance at the initially unknown number of sampled configurations associated with each step. It is a method of incremental precomputation, fast because it takes advantage of the sample

  7. Error behavior of multistep methods applied to unstable differential systems

    NASA Technical Reports Server (NTRS)

    Brown, R. L.

    1977-01-01

    The problem of modeling a dynamic system described by a system of ordinary differential equations which has unstable components for limited periods of time is discussed. It is shown that the global error in a multistep numerical method is the solution to a difference equation initial value problem, and the approximate solution is given for several popular multistep integration formulas. Inspection of the solution leads to the formulation of four criteria for integrators appropriate to unstable problems. A sample problem is solved numerically using three popular formulas and two different stepsizes to illustrate the appropriateness of the criteria.

  8. INDES User's guide multistep input design with nonlinear rotorcraft modeling

    NASA Technical Reports Server (NTRS)

    1979-01-01

    The INDES computer program, a multistep input design program used as part of a data processing technique for rotorcraft systems identification, is described. Flight test inputs base on INDES improve the accuracy of parameter estimates. The input design algorithm, program input, and program output are presented.

  9. A Multistep Synthesis for an Advanced Undergraduate Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Chang Ji; Peters, Dennis G.

    2006-01-01

    Multistep syntheses are often important components of the undergraduate organic laboratory experience and a three-step synthesis of 5-(2-sulfhydrylethyl) salicylaldehyde was described. The experiment is useful as a special project for an advanced undergraduate organic chemistry laboratory course and offers opportunities for students to master a…

  10. 48 CFR 15.202 - Advisory multi-step process.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... process. 15.202 Section 15.202 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION... Information 15.202 Advisory multi-step process. (a) The agency may publish a presolicitation notice (see 5.204... concept, past performance, and limited pricing information). At a minimum, the notice shall...

  11. 48 CFR 15.202 - Advisory multi-step process.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... process. 15.202 Section 15.202 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION... Information 15.202 Advisory multi-step process. (a) The agency may publish a presolicitation notice (see 5.204... concept, past performance, and limited pricing information). At a minimum, the notice shall...

  12. 48 CFR 15.202 - Advisory multi-step process.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... process. 15.202 Section 15.202 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION... Information 15.202 Advisory multi-step process. (a) The agency may publish a presolicitation notice (see 5.204... concept, past performance, and limited pricing information). At a minimum, the notice shall...

  13. 48 CFR 15.202 - Advisory multi-step process.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... process. 15.202 Section 15.202 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION... Information 15.202 Advisory multi-step process. (a) The agency may publish a presolicitation notice (see 5.204... concept, past performance, and limited pricing information). At a minimum, the notice shall...

  14. Multistep and Multistage Boundary Integral Methods for the Wave Equation

    NASA Astrophysics Data System (ADS)

    Banjai, Lehel

    2009-09-01

    We describe how time-discretized wave equation in a homogeneous medium can be solved by boundary integral methods. The time discretization can be a multistep, Runge-Kutta, or a more general multistep-multistage method. The resulting convolutional system of boundary integral equations falls in the family of convolution quadratures of Ch. Lubich. In this work our aim is to discuss a new technique for efficiently solving the discrete convolutional system and to present large scale 3D numerical experiments with a wide range of time-discretizations that have up to now not appeared in print. One of the conclusions is that Runge-Kutta methods are often the method of choice even at low accuracy; yet, in connection with hyperbolic problems BDF (backward difference formulas) have been predominant in the literature on convolution quadrature.

  15. A multistep approach for infrared face recognition in texture space

    NASA Astrophysics Data System (ADS)

    Akhloufi, Moulay A.; Bendada, Abdelhakim

    2013-05-01

    Face recognition is an area of computer vision that has attracted a lot of interest from the research community. A growing demand for robust face recognition in security applications has driven interesting advancements in this field. In this work, we introduce a new multistep approach for face recognition in the infrared spectrum. The proposed approach works in texture space using binary and ternary pattern descriptors. The approach operates in two steps. In the first step, dimensionality reduction techniques are used to classify the preprocessed infrared face image. This operation permits the selection of the highest score candidates. In the second step, a small set of these candidates are then classified using a correlation based approach. This last step permits the selection of the best matching candidate. The obtained results show a high increase in the face recognition performance when a multistep approach is used compared to dimensionality reduction face recognition techniques alone.

  16. The Application of Baum-Welch Algorithm in Multistep Attack

    PubMed Central

    Zhang, Yanxue; Zhao, Dongmei; Liu, Jinxing

    2014-01-01

    The biggest difficulty of hidden Markov model applied to multistep attack is the determination of observations. Now the research of the determination of observations is still lacking, and it shows a certain degree of subjectivity. In this regard, we integrate the attack intentions and hidden Markov model (HMM) and support a method to forecasting multistep attack based on hidden Markov model. Firstly, we train the existing hidden Markov model(s) by the Baum-Welch algorithm of HMM. Then we recognize the alert belonging to attack scenarios with the Forward algorithm of HMM. Finally, we forecast the next possible attack sequence with the Viterbi algorithm of HMM. The results of simulation experiments show that the hidden Markov models which have been trained are better than the untrained in recognition and prediction. PMID:24991642

  17. Shaping of the Root Canal System: A Multistep Technique.

    PubMed

    Gallottini, Livio

    2017-09-01

    The aim of this scientific work is to illustrate the technique of shaping the root canal system using the multistep technique. Over time, various endodontic instrumentation techniques have been put forward, from the "step-back" technique (apical-coronal) to the "crown-down" technique (coronal-apical), the "double-flared" technique, and the most recent "single-length" technique. The multistep technique involves six steps, one of the main objectives of these being the safety of the use of mechanical instruments with a reduction in the risk that they fracture. This technique ("mixed") provides for the use of both manual instruments in stainless steel and mechanical instruments in nickel titanium (Ni-Ti). The multistep technique is based on a standardized, flexible, and clinical protocol, which can provide for a reduction in the number of endodontic passages and instruments used and, therefore, a simplification of the operating procedure depending on both the difficulty of the root canals and the competence of the operator. This technique is a technique for shaping the endodontic space that allows the set objectives of endodontic therapy to be reached in a predictable way with a reduced risk of iatrogenic complications.

  18. Optimal installation locations for automated external defibrillators in Taipei 7-Eleven stores: using GIS and a genetic algorithm with a new stirring operator.

    PubMed

    Huang, Chung-Yuan; Wen, Tzai-Hung

    2014-01-01

    Immediate treatment with an automated external defibrillator (AED) increases out-of-hospital cardiac arrest (OHCA) patient survival potential. While considerable attention has been given to determining optimal public AED locations, spatial and temporal factors such as time of day and distance from emergency medical services (EMSs) are understudied. Here we describe a geocomputational genetic algorithm with a new stirring operator (GANSO) that considers spatial and temporal cardiac arrest occurrence factors when assessing the feasibility of using Taipei 7-Eleven stores as installation locations for AEDs. Our model is based on two AED conveyance modes, walking/running and driving, involving service distances of 100 and 300 meters, respectively. Our results suggest different AED allocation strategies involving convenience stores in urban settings. In commercial areas, such installations can compensate for temporal gaps in EMS locations when responding to nighttime OHCA incidents. In residential areas, store installations can compensate for long distances from fire stations, where AEDs are currently held in Taipei.

  19. Approach to automation in immunohistochemistry.

    PubMed

    Moreau, A; Le Neel, T; Joubert, M; Truchaud, A; Laboisse, C

    1998-12-01

    The introduction of immunochemical techniques into the routine pathology laboratory has significantly expanded the capabilities of the pathologist in diagnostic procedures. Immunostaining represents a powerful diagnostic tool in the identification and localization of cellular antigens, in paraffin sections, frozen tissues and cell preparations. The labeled-streptavidin-biotin method provides excellent sensitivity and performance. This multistep procedure includes: incubation of the slide with primary antibody, reaction with the biotinylated secondary antibody, binding with an enzyme conjugated streptavidin and revelation with chromogen substrate. Evaluation of the finished product is directly dependent on the quality of the technique. The main critical steps of this manual method are reagents application, incubation times and rinsing. These steps could be accessible to automation. Automation in immunohistochemistry could guarantee a continuous quality of labelling in improving standardisation, optimization and traceability of operations. The required qualifications are analytical flexibility, low cost, walkaway operation, user-friendly interface and biosafety.

  20. Fully automated sample preparation microsystem for genetic testing of hereditary hearing loss using two-color multiplex allele-specific PCR.

    PubMed

    Zhuang, Bin; Gan, Wupeng; Wang, Shuaiqin; Han, Junping; Xiang, Guangxin; Li, Cai-Xia; Sun, Jing; Liu, Peng

    2015-01-20

    A fully automated microsystem consisting of a disposable DNA extraction and PCR microchip, as well as a compact control instrument, has been successfully developed for genetic testing of hereditary hearing loss from human whole blood. DNA extraction and PCR were integrated into a single 15-μL reaction chamber, where a piece of filter paper was embedded for capturing genomic DNA, followed by in-situ PCR amplification without elution. Diaphragm microvalves actuated by external solenoids together with a "one-way" fluidic control strategy operated by a modular valve positioner and a syringe pump were employed to control the fluids and to seal the chamber during thermal cycling. Fully automated DNA extractions from as low as 0.3-μL human whole blood followed by amplifications of 59-bp β-actin fragments can be completed on the microsystem in about 100 min. Negative control tests that were performed between blood sample analyses proved the successful elimination of any contamination or carryover in the system. To more critically test the microsystem, a two-color multiplex allele-specific PCR (ASPCR) assay for detecting c.176_191del16, c.235delC, and c.299_300delAT mutations in GJB2 gene that accounts for hereditary hearing loss was constructed. Two allele-specific primers, one labeled with TAMRA for wild type and the other with FAM for mutation, were designed for each locus. DNA extraction from blood and ASPCR were performed on the microsystem, followed by an electrophoretic analysis on a portable microchip capillary electrophoresis system. Blood samples from a healthy donor and five persons with genetic mutations were all accurately analyzed with only two steps in less than 2 h.

  1. Event-triggered logical flow control for comprehensive process integration of multi-step assays on centrifugal microfluidic platforms.

    PubMed

    Kinahan, David J; Kearney, Sinéad M; Dimov, Nikolay; Glynn, Macdara T; Ducrée, Jens

    2014-07-07

    The centrifugal "lab-on-a-disc" concept has proven to have great potential for process integration of bioanalytical assays, in particular where ease-of-use, ruggedness, portability, fast turn-around time and cost efficiency are of paramount importance. Yet, as all liquids residing on the disc are exposed to the same centrifugal field, an inherent challenge of these systems remains the automation of multi-step, multi-liquid sample processing and subsequent detection. In order to orchestrate the underlying bioanalytical protocols, an ample palette of rotationally and externally actuated valving schemes has been developed. While excelling with the level of flow control, externally actuated valves require interaction with peripheral instrumentation, thus compromising the conceptual simplicity of the centrifugal platform. In turn, for rotationally controlled schemes, such as common capillary burst valves, typical manufacturing tolerances tend to limit the number of consecutive laboratory unit operations (LUOs) that can be automated on a single disc. In this paper, a major advancement on recently established dissolvable film (DF) valving is presented; for the very first time, a liquid handling sequence can be controlled in response to completion of preceding liquid transfer event, i.e. completely independent of external stimulus or changes in speed of disc rotation. The basic, event-triggered valve configuration is further adapted to leverage conditional, large-scale process integration. First, we demonstrate a fluidic network on a disc encompassing 10 discrete valving steps including logical relationships such as an AND-conditional as well as serial and parallel flow control. Then we present a disc which is capable of implementing common laboratory unit operations such as metering and selective routing of flows. Finally, as a pilot study, these functions are integrated on a single disc to automate a common, multi-step lab protocol for the extraction of total RNA from

  2. Automated discovery of structural features of the optic nerve head on the basis of image and genetic data

    NASA Astrophysics Data System (ADS)

    Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

    2014-03-01

    Evaluation of optic nerve head (ONH) structure is a commonly used clinical technique for both diagnosis and monitoring of glaucoma. Glaucoma is associated with characteristic changes in the structure of the ONH. We present a method for computationally identifying ONH structural features using both imaging and genetic data from a large cohort of participants at risk for primary open angle glaucoma (POAG). Using 1054 participants from the Ocular Hypertension Treatment Study, ONH structure was measured by application of a stereo correspondence algorithm to stereo fundus images. In addition, the genotypes of several known POAG genetic risk factors were considered for each participant. ONH structural features were discovered using both a principal component analysis approach to identify the major modes of variance within structural measurements and a linear discriminant analysis approach to capture the relationship between genetic risk factors and ONH structure. The identified ONH structural features were evaluated based on the strength of their associations with genotype and development of POAG by the end of the OHTS study. ONH structural features with strong associations with genotype were identified for each of the genetic loci considered. Several identified ONH structural features were significantly associated (p < 0.05) with the development of POAG after Bonferroni correction. Further, incorporation of genetic risk status was found to substantially increase performance of early POAG prediction. These results suggest incorporating both imaging and genetic data into ONH structural modeling significantly improves the ability to explain POAG-related changes to ONH structure.

  3. Genetics

    MedlinePlus

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  4. Multistep ion exchange processes of gradient refractive index rod lens.

    PubMed

    Lv, Hao; Liu, Aimei; Tong, Jufang; Yi, Xunong; Li, Qianguang; Wang, Xinmin; Ding, Yaoming

    2011-01-01

    A mathematical model for research on the refractive index profile (RIP) of multistep ion exchange processes (IEPs) of gradient refractive index rod lenses (GRINs) is established by the different initial condition and boundary condition, based on the Fickian diffusion equation. GRIN rod lenses have been fabricated using the three-step IEPs. Research results indicate that the experimental deviations of refractive index (DRI) are in good agreement with the theoretical data. The DRI of three-step IEPs is superior to the one- and two-step IEPs and smaller than 10(-5).

  5. Power transmission coefficients for multi-step index optical fibres.

    PubMed

    Aldabaldetreku, Gotzon; Zubia, Joseba; Durana, Gaizka; Arrue, Jon

    2006-02-20

    The aim of the present paper is to provide a single analytical expression of the power transmission coefficient for leaky rays in multi-step index (MSI) fibres. This expression is valid for all tunnelling and refracting rays and allows us to evaluate numerically the power attenuation along an MSI fibre of an arbitrary number of layers. We validate our analysis by comparing the results obtained for limit cases of MSI fibres with those corresponding to step-index (SI) and graded-index (GI) fibres. We also make a similar comparison between this theoretical expression and the use of the WKB solutions of the scalar wave equation.

  6. Microwaves in drug discovery and multi-step synthesis.

    PubMed

    Alexandre, François-René; Domon, Lisianne; Frère, Stéphane; Testard, Alexandra; Thiéry, Valérie; Besson, Thierry

    2003-01-01

    The interest of microwaves in drug discovery and multi-step synthesis is exposed with the aim of describing our strategy. These studies are connected with our work on the synthesis of original heterocyclic compounds with potential pharmaceutical value. Reactions in the presence of solvent and solvent-free synthesis can be realised under a variety of conditions; for some of these selected results are given, and where available, results from comparison with the same solvent-free conditions but with classical heating are given.

  7. Modeling biology with HDL languages: a first step toward a genetic design automation tool inspired from microelectronics.

    PubMed

    Gendrault, Yves; Madec, Morgan; Lallement, Christophe; Haiech, Jacques

    2014-04-01

    Nowadays, synthetic biology is a hot research topic. Each day, progresses are made to improve the complexity of artificial biological functions in order to tend to complex biodevices and biosystems. Up to now, these systems are handmade by bioengineers, which require strong technical skills and leads to nonreusable development. Besides, scientific fields that share the same design approach, such as microelectronics, have already overcome several issues and designers succeed in building extremely complex systems with many evolved functions. On the other hand, in systems engineering and more specifically in microelectronics, the development of the domain has been promoted by both the improvement of technological processes and electronic design automation tools. The work presented in this paper paves the way for the adaptation of microelectronics design tools to synthetic biology. Considering the similarities and differences between the synthetic biology and microelectronics, the milestones of this adaptation are described. The first one concerns the modeling of biological mechanisms. To do so, a new formalism is proposed, based on an extension of the generalized Kirchhoff laws to biology. This way, a description of all biological mechanisms can be made with languages widely used in microelectronics. Our approach is therefore successfully validated on specific examples drawn from the literature.

  8. Multigeometry Nanoparticle Engineering via Kinetic Control through Multistep assembly

    NASA Astrophysics Data System (ADS)

    Chen, Yingchao; Wang, Xiaojun; Zhang, Ke; Zhang, Fuwu; Mays, Jimmy; Wooley, Karen; Pochan, Darrin

    2014-03-01

    Organization of block copolymers into complicated multicompartment (MCM) and multigeometry (MGM) nanostructures is of increasing interest. Multistep, co-assembly methods resulting in kinetic control processing was used to produce complex nanoparticles that are not obtained via other assembly methods. Vesicle-cylinder, separate vesicle and cylinder, disk-cylinder, and mixed vesicle nanoparticles were constructed by binary blends of distinct diblock copolymers. Initially, the vesicle former polyacrylic acid-polyisoprene and cylinder former polyacrylic acid-polystyrene which share the same hydrophilic domain but immiscible hydrophobic domain were blended in THF. Secondly, dimaine molecules are added to associate with the common hydrophilic PAA. Importantly, and lastly, by tuning the kinetic addition rate of selective, miscible solvent water, the unlike hydrophobic blocks are kinetically trapped into one particle and eventually nanophase separate to form multiple compartments and multigeometries. The effective bottom-up multistep assembly strategies can be applied in other binary/ternary blends, in which new vesicle-sphere, disk-disk and cylinder-cylinder MCM/MGM nanoparticles were programed. We are grateful for the financial support from the National Science Funding DMR-0906815 (D.J.P. and K.L.W.) and NIST METROLOGY POCHAN 2012.

  9. Performance of "look-ahead" linear multistep methods

    NASA Astrophysics Data System (ADS)

    Mitsui, Taketomo

    2016-06-01

    We are concerned with the initial-value problem of ordinary differential equations (ODEs). LALMM, which stands for "look-ahead" linear multistep methods, is a new class among the discrete variable methods (DVMs) for the problem. Here we refer DVMs to the methods which yield a sequence of approximations yn ≈ y(xn) on the set of points xn+1 = xn + hn (n = 0, 1, 2, …). Along with the look-for value yn+k and the back-values yn, yn+1, …, yn+k-1, we include the look-ahead value yn+k+1 in the stepping mechanism of the method upon the equi-distant step points {xn}. By employing two different linear multistep schemes, we approximate the look-for value with the predictor-corrector iteration. The core issue of numerical analysis of new methods is whether they can perform better than the existing methods. We derived several LALMM schemes of two-step (k = 2) family (LALTM) and examine their performance through test examples of ODEs. We will report their test results by several numerical examples and describe a possible way to overcome their difficulties shown in the examples.

  10. Adaptation to vocal expressions reveals multistep perception of auditory emotion.

    PubMed

    Bestelmeyer, Patricia E G; Maurage, Pierre; Rouger, Julien; Latinus, Marianne; Belin, Pascal

    2014-06-11

    The human voice carries speech as well as important nonlinguistic signals that influence our social interactions. Among these cues that impact our behavior and communication with other people is the perceived emotional state of the speaker. A theoretical framework for the neural processing stages of emotional prosody has suggested that auditory emotion is perceived in multiple steps (Schirmer and Kotz, 2006) involving low-level auditory analysis and integration of the acoustic information followed by higher-level cognition. Empirical evidence for this multistep processing chain, however, is still sparse. We examined this question using functional magnetic resonance imaging and a continuous carry-over design (Aguirre, 2007) to measure brain activity while volunteers listened to non-speech-affective vocalizations morphed on a continuum between anger and fear. Analyses dissociated neuronal adaptation effects induced by similarity in perceived emotional content between consecutive stimuli from those induced by their acoustic similarity. We found that bilateral voice-sensitive auditory regions as well as right amygdala coded the physical difference between consecutive stimuli. In contrast, activity in bilateral anterior insulae, medial superior frontal cortex, precuneus, and subcortical regions such as bilateral hippocampi depended predominantly on the perceptual difference between morphs. Our results suggest that the processing of vocal affect recognition is a multistep process involving largely distinct neural networks. Amygdala and auditory areas predominantly code emotion-related acoustic information while more anterior insular and prefrontal regions respond to the abstract, cognitive representation of vocal affect.

  11. Adaptation to Vocal Expressions Reveals Multistep Perception of Auditory Emotion

    PubMed Central

    Maurage, Pierre; Rouger, Julien; Latinus, Marianne; Belin, Pascal

    2014-01-01

    The human voice carries speech as well as important nonlinguistic signals that influence our social interactions. Among these cues that impact our behavior and communication with other people is the perceived emotional state of the speaker. A theoretical framework for the neural processing stages of emotional prosody has suggested that auditory emotion is perceived in multiple steps (Schirmer and Kotz, 2006) involving low-level auditory analysis and integration of the acoustic information followed by higher-level cognition. Empirical evidence for this multistep processing chain, however, is still sparse. We examined this question using functional magnetic resonance imaging and a continuous carry-over design (Aguirre, 2007) to measure brain activity while volunteers listened to non-speech-affective vocalizations morphed on a continuum between anger and fear. Analyses dissociated neuronal adaptation effects induced by similarity in perceived emotional content between consecutive stimuli from those induced by their acoustic similarity. We found that bilateral voice-sensitive auditory regions as well as right amygdala coded the physical difference between consecutive stimuli. In contrast, activity in bilateral anterior insulae, medial superior frontal cortex, precuneus, and subcortical regions such as bilateral hippocampi depended predominantly on the perceptual difference between morphs. Our results suggest that the processing of vocal affect recognition is a multistep process involving largely distinct neural networks. Amygdala and auditory areas predominantly code emotion-related acoustic information while more anterior insular and prefrontal regions respond to the abstract, cognitive representation of vocal affect. PMID:24920615

  12. Multistep carcinogenesis in the formation of basal cell carcinoma of the skin

    SciTech Connect

    Gailani, M.; Leffell, D.; Ziegler, A.

    1994-09-01

    Basal cell carcinoma of the skin (BCC) is the most common cancer in humans, a slow growing tumor whose incidence strongly correlates with exposure to UV light. Although the molecular basis of BCC formation is not well understood, loss of heterozygosity (LOH) for markers on chromosome 9q in 70% of BCCs suggests that inactivation of a tumor suppressor on 9q22 is an important early step. UV induced mutations in the p53 gene have also been found in over 50% of sporadic BCCs. We analyzed 18 sporadic BCCs for allelic loss on chromosome 9 and point mutations in the p53 gene and attempted to correlate genetic alteration with pathological subtype and relative UV light exposure. Eight of eighteen tumors (45%) showed LOH on chromosome 9 as well as point mutation of the p53 gene, three of eighteen tumors (17%) showed mutation of the p53 gene without LOH on chromosome 9, five of eighteen tumors (27%) showed LOH for chromosome 9 without evidence of mutation in the p53 gene, and two of eighteen tumors (11%) showed neither LOH on chromosome 9 nor mutation in the p53 gene. Tumor pathology showed no obvious correlation between mutation and tumor aggressiveness. However, one tumor of a unique, aggressive growth subtype had no genetic alteration suggesting a different genetic mechanism in this particular subgroup. 38% of tumors from areas of greatest sun-exposure showed both mutations. The data suggests a strong correlation between inactivation of a tumor suppressor gene on chromosome 9 and mutation in the p53 gene though the sequence of events cannot be determined. Because carcinogenesis is a multistep process and genetic injury from UV light is only one factor, further correlation with degree of tumor differentiation may clarify the genetic process in BCCs.

  13. Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches.

    PubMed

    Hartmann, Martin; Frey, Beat; Kölliker, Roland; Widmer, Franco

    2005-06-01

    Cultivation independent analyses of soil microbial community structures are frequently used to describe microbiological soil characteristics. This approach is based on direct extraction of total soil DNA followed by PCR amplification of selected marker genes and subsequent genetic fingerprint analyses. Semi-automated genetic fingerprinting techniques such as terminal restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA) yield high-resolution patterns of highly diverse soil microbial communities and hold great potential for use in routine soil quality monitoring, when rapid high throughput screening for differences or changes is more important than phylogenetic identification of organisms affected. Our objective was to perform profound statistical analysis to evaluate the cultivation independent approach and the consistency of results from T-RFLP and RISA. As a model system, we used two different heavy metal treated soils from an open top chamber experiment. Bacterial T-RFLP and RISA profiles of 16S rDNA were converted into numeric data matrices in order to allow for detailed statistical analyses with cluster analysis, Mantel test statistics, Monte Carlo permutation tests and ANOVA. Analyses revealed that soil DNA-contents were significantly correlated with soil microbial biomass in our system. T-RFLP and RISA yielded highly consistent and correlating results and both allowed to distinguish the four treatments with equal significance. While RISA represents a fast and general fingerprinting method of moderate cost and labor intensity, T-RFLP is technically more demanding but offers the advantage of phylogenetic identification of detected soil microorganisms. Therefore, selection of either of these methods should be based on the specific research question under investigation.

  14. Vitamin B12 transport from food to the body's cells--a sophisticated, multistep pathway.

    PubMed

    Nielsen, Marianne J; Rasmussen, Mie R; Andersen, Christian B F; Nexø, Ebba; Moestrup, Søren K

    2012-05-01

    Vitamin B(12) (B(12); also known as cobalamin) is a cofactor in many metabolic processes; deficiency of this vitamin is associated with megaloblastic anaemia and various neurological disorders. In contrast to many prokaryotes, humans and other mammals are unable to synthesize B(12). Instead, a sophisticated pathway for specific uptake and transport of this molecule has evolved. Failure in the gastrointestinal part of this pathway is the most common cause of nondietary-induced B(12) deficiency disease. However, although less frequent, defects in cellular processing and further downstream steps in the transport pathway are also known culprits of functional B(12) deficiency. Biochemical and genetic approaches have identified novel proteins in the B(12) transport pathway--now known to involve more than 15 gene products--delineating a coherent pathway for B(12) trafficking from food to the body's cells. Some of these gene products are specifically dedicated to B(12) transport, whereas others embrace additional roles, which explains the heterogeneity in the clinical picture of the many genetic disorders causing B(12) deficiency. This Review describes basic and clinical features of this multistep pathway with emphasis on gastrointestinal transport of B(12) and its importance in clinical medicine.

  15. An ordinary differential equation model for the multistep transformation to cancer.

    PubMed

    Spencer, Sabrina L; Berryman, Matthew J; García, José A; Abbott, Derek

    2004-12-21

    Cancer is viewed as a multistep process whereby a normal cell is transformed into a cancer cell through the acquisition of mutations. We reduce the complexities of cancer progression to a simple set of underlying rules that govern the transformation of normal cells to malignant cells. In doing so, we derive an ordinary differential equation model that explores how the balance of angiogenesis, cell death rates, genetic instability, and replication rates give rise to different kinetics in the development of cancer. The key predictions of the model are that cancer develops fastest through a particular ordering of mutations and that mutations in genes that maintain genomic integrity would be the most deleterious type of mutations to inherit. In addition, we perform a sensitivity analysis on the parameters included in the model to determine the probable contribution of each. This paper presents a novel approach to viewing the genetic basis of cancer from a systems biology perspective and provides the groundwork for other models that can be directly tied to clinical and molecular data.

  16. Slotting optimization of automated storage and retrieval system (AS/RS) for efficient delivery of parts in an assembly shop using genetic algorithm: A case Study

    NASA Astrophysics Data System (ADS)

    Yue, L.; Guan, Z.; He, C.; Luo, D.; Saif, U.

    2017-06-01

    In recent years, the competitive pressure on manufacturing companies shifted them from mass production to mass customization to produce large variety of products. It is a great challenge for companies nowadays to produce customized mixed flow mode of production to meet customized demand on time. Due to large variety of products, the storage system to deliver variety of products to production lines influences on the timely production of variety of products, as investigated from by simulation study of an inefficient storage system of a real Company, in the current research. Therefore, current research proposed a slotting optimization model with mixed model sequence to assemble in consideration of the final flow lines to optimize whole automated storage and retrieval system (AS/RS) and distribution system in the case company. Current research is aimed to minimize vertical height of centre of gravity of AS/RS and total time spent for taking the materials out from the AS/RS simultaneously. Genetic algorithm is adopted to solve the proposed problem and computational result shows significant improvement in stability and efficiency of AS/RS as compared to the existing method used in the case company.

  17. Autonomous Multistep Organic Synthesis in a Single Isothermal Solution Mediated by a DNA Walker

    PubMed Central

    He, Yu; Liu, David R.

    2010-01-01

    Multistep synthesis in the laboratory typically requires numerous reaction vessels, each containing a different set of reactants. In contrast, cells are capable of performing highly efficient and selective multistep biosynthesis under mild conditions with all reactants simultaneously present in solution. If the latter approach could be applied in the laboratory, it may improve the ease, speed, and efficiency of multistep reaction sequences. Here we show that a DNA mechanical device— a DNA walker moving along a DNA track— can be used to perform a series of amine acylation reactions in a single solution without any external intervention. The multistep products generated by this primitive ribosome mimetic are programmed by the sequence of the DNA track, are unrelated to the structure of DNA, and are formed with speeds and overall yields significantly greater than those previously achieved by multistep DNA-templated small-molecule synthesis. PMID:20935654

  18. Multi-step prediction of physiological tremor for robotics applications.

    PubMed

    Veluvolu, K C; Tatinati, S; Hong, S M; Ang, W T

    2013-01-01

    The performance of surgical robotic devices in real-time mainly depends on phase-delay in sensors and filtering process. A phase delay of 16-20 ms is unavoidable in these robotics procedures due to the presence of hardware low pass filter in sensors and pre-filtering required in later stages of cancellation. To overcome this phase delay, we employ multi-step prediction with band limited multiple Fourier linear combiner (BMFLC) and Autoregressive (AR) methods. Results show that the overall accuracy is improved by 60% for tremor estimation compared to single-step prediction methods in the presence of phase delay. Experimental results with the proposed methods for 1-DOF tremor estimation highlight the improvement.

  19. Global model including multistep ionizations in helium plasmas

    NASA Astrophysics Data System (ADS)

    Oh, Seung-Ju; Lee, Hyo-Chang; Chung, Chin-Wook

    2016-12-01

    Particle and power balance equations including stepwise ionizations are derived and solved in helium plasmas. In the balance equations, two metastable states (21S1 in singlet and 23S1 triplet) are considered and the followings are obtained. The plasma density linearly increases and the electron temperature is relatively in a constant value against the absorbed power. It is also found that the contribution to multi-step ionization with respect to the single-step ionization is in the range of 8%-23%, as the gas pressure increases from 10 mTorr to 100 mTorr. Compared to the results in the argon plasma, there is little variation in the collisional energy loss per electron-ion pair created (ɛc) with absorbed power and gas pressure due to the small collision cross section and higher inelastic collision threshold energy.

  20. Multistep prediction of physiological tremor for surgical robotics applications.

    PubMed

    Veluvolu, Kalyana C; Tatinati, Sivanagaraja; Hong, Sun-Mog; Ang, Wei Tech

    2013-11-01

    Accurate canceling of physiological tremor is extremely important in robotics-assisted surgical instruments/procedures. The performance of robotics-based hand-held surgical devices degrades in real time due to the presence of phase delay in sensors (hardware) and filtering (software) processes. Effective tremor compensation requires zero-phase lag in filtering process so that the filtered tremor signal can be used to regenerate an opposing motion in real time. Delay as small as 20 ms degrades the performance of human-machine interference. To overcome this phase delay, we employ multistep prediction in this paper. Combined with the existing tremor estimation methods, the procedure improves the overall accuracy by 60% for tremor estimation compared to single-step prediction methods in the presence of phase delay. Experimental results with developed methods for 1-DOF tremor estimation highlight the improvement.

  1. Controlled multistep synthesis in a three-phase droplet reactor

    PubMed Central

    Nightingale, Adrian M.; Phillips, Thomas W.; Bannock, James H.; de Mello, John C.

    2014-01-01

    Channel-fouling is a pervasive problem in continuous flow chemistry, causing poor product control and reactor failure. Droplet chemistry, in which the reaction mixture flows as discrete droplets inside an immiscible carrier liquid, prevents fouling by isolating the reaction from the channel walls. Unfortunately, the difficulty of controllably adding new reagents to an existing droplet stream has largely restricted droplet chemistry to simple reactions in which all reagents are supplied at the time of droplet formation. Here we describe an effective method for repeatedly adding controlled quantities of reagents to droplets. The reagents are injected into a multiphase fluid stream, comprising the carrier liquid, droplets of the reaction mixture and an inert gas that maintains a uniform droplet spacing and suppresses new droplet formation. The method, which is suited to many multistep reactions, is applied to a five-stage quantum dot synthesis wherein particle growth is sustained by repeatedly adding fresh feedstock. PMID:24797034

  2. Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations

    PubMed Central

    Tong, Mark Y.; Cassa, Christopher A.; Kohane, Isaac S.

    2011-01-01

    Summary: Accurate annotations of genomic variants are necessary to achieve full-genome clinical interpretations that are scientifically sound and medically relevant. Many disease associations, especially those reported before the completion of the HGP, are limited in applicability because of potential inconsistencies with our current standards for genomic coordinates, nomenclature and gene structure. In an effort to validate and link variants from the medical genetics literature to an unambiguous reference for each variant, we developed a software pipeline and reviewed 68 641 single amino acid mutations from Online Mendelian Inheritance in Man (OMIM), Human Gene Mutation Database (HGMD) and dbSNP. The frequency of unresolved mutation annotations varied widely among the databases, ranging from 4 to 23%. A taxonomy of primary causes for unresolved mutations was produced. Availability: This program is freely available from the web site (http://safegene.hms.harvard.edu/aa2nt/). Contact: mt153@hms.harvard.edu; mark_tong2009@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21258063

  3. Multi-objective genetic algorithm for the automated planning of a wireless sensor network to monitor a critical facility

    NASA Astrophysics Data System (ADS)

    Jourdan, Damien B.; de Weck, Olivier L.

    2004-09-01

    This paper examines the optimal placement of nodes for a Wireless Sensor Network (WSN) designed to monitor a critical facility in a hostile region. The sensors are dropped from an aircraft, and they must be connected (directly or via hops) to a High Energy Communication Node (HECN), which serves as a relay from the ground to a satellite or a high-altitude aircraft. The sensors are assumed to have fixed communication and sensing ranges. The facility is modeled as circular and served by two roads. This simple model is used to benchmark the performance of the optimizer (a Multi-Objective Genetic Algorithm, or MOGA) in creating WSN designs that provide clear assessments of movements in and out of the facility, while minimizing both the likelihood of sensors being discovered and the number of sensors to be dropped. The algorithm is also tested on two other scenarios; in the first one the WSN must detect movements in and out of a circular area, and in the second one it must cover uniformly a square region. The MOGA is shown again to perform well on those scenarios, which shows its flexibility and possible application to more complex mission scenarios with multiple and diverse targets of observation.

  4. Evidence that the RdeA protein is a component of a multistep phosphorelay modulating rate of development in Dictyostelium.

    PubMed Central

    Chang, W T; Thomason, P A; Gross, J D; Neweil, P C

    1998-01-01

    We have isolated an insertional mutant of Dictyostelium discoideum that aggregated rapidly and formed spores and stalk cells within 14 h of development instead of the normal 24 h. We have shown by parasexual genetics that the insertion is in the rdeA locus and have cloned the gene. It encodes a predicted 28 kDa protein (RdeA) that is enriched in charged residues and is very hydrophilic. Constructs with the DNA for the c-Myc epitope or for the green fluorescent protein indicate that RdeA is not compartmentalized. RdeA displays homology around a histidine residue at amino acid 65 with members of the H2 module family of phosphotransferases that participate in multistep phosphoryl relays. Replacement of this histidine rendered the protein inactive. The mutant is complemented by transformation with the Ypd1 gene of Saccharomyces cerevisiae, itself an H2 module protein. We propose that RdeA is part of a multistep phosphorelay system that modulates the rate of development. PMID:9582274

  5. Space station automation study: Automation requirements derived from space manufacturing concepts. Volume 1: Executive summary

    NASA Technical Reports Server (NTRS)

    1984-01-01

    The electroepitaxial process and the Very Large Scale Integration (VLSI) circuits (chips) facilities were chosen because each requires a very high degree of automation, and therefore involved extensive use of teleoperators, robotics, process mechanization, and artificial intelligence. Both cover a raw materials process and a sophisticated multi-step process and are therfore highly representative of the kinds of difficult operation, maintenance, and repair challenges which can be expected for any type of space manufacturing facility. Generic areas were identified which will require significant further study. The initial design will be based on terrestrial state-of-the-art hard automation. One hundred candidate missions were evaluated on the basis of automation portential and availability of meaning ful knowldege. The design requirements and unconstrained design concepts developed for the two missions are presented.

  6. Stable hydrogen isotopic analysis of nanomolar molecular hydrogen by automatic multi-step gas chromatographic separation.

    PubMed

    Komatsu, Daisuke D; Tsunogai, Urumu; Kamimura, Kanae; Konno, Uta; Ishimura, Toyoho; Nakagawa, Fumiko

    2011-11-15

    We have developed a new automated analytical system that employs a continuous flow isotope ratio mass spectrometer to determine the stable hydrogen isotopic composition (δD) of nanomolar quantities of molecular hydrogen (H(2)) in an air sample. This method improves previous methods to attain simpler and lower-cost analyses, especially by avoiding the use of expensive or special devices, such as a Toepler pump, a cryogenic refrigerator, and a special evacuation system to keep the temperature of a coolant under reduced pressure. Instead, the system allows H(2) purification from the air matrix via automatic multi-step gas chromatographic separation using the coolants of both liquid nitrogen (77 K) and liquid nitrogen + ethanol (158 K) under 1 atm pressure. The analytical precision of the δD determination using the developed method was better than 4‰ for >5 nmol injections (250 mL STP for 500 ppbv air sample) and better than 15‰ for 1 nmol injections, regardless of the δD value, within 1 h for one sample analysis. Using the developed system, the δD values of H(2) can be quantified for atmospheric samples as well as samples of representative sources and sinks including those containing small quantities of H(2) , such as H(2) in soil pores or aqueous environments, for which there is currently little δD data available. As an example of such trace H(2) analyses, we report here the isotope fractionations during H(2) uptake by soils in a static chamber. The δD values of H(2) in these H(2)-depleted environments can be useful in constraining the budgets of atmospheric H(2) by applying an isotope mass balance model.

  7. Multistep processing and stress reduction in CVD diamond films

    NASA Astrophysics Data System (ADS)

    Nijhawan, Sumit

    A serious impediment in the utility of diamond films is the large internal stresses that develop during growth. These stresses generally have thermal and growth components. The thermal component is determined by the mismatch in thermal expansion coefficients of film and substrate while the growth component may arise from several possible mechanisms during CVD growth. These growth stresses tend to be particularly large in diamond. The objective of this work is to understand and reduce the growth stresses in diamond films by tailoring the CVD process. Continuous, polycrystalline diamond films were deposited on Si by microwave plasma-assisted CVD. Very high internal stresses (>2 GPA) consisting of growth and thermal components were observed. The growth component is tensile and increases with growth time. We were able to reduce the evolution of growth stresses considerably by multistep processing of our films. An intermediate annealing step was included between successive growth periods. It is important to note that the annealing step must be conducted at key points during the growth process in order to effectively reduce stress. Maximum reduction in stress is achieved only if the sample is annealed when the diamond grains are partially coalesced (after 2--3 hours of growth). Annealing of continuous films does not produce a significant reduction in stress. The origin of growth stress in our films is attributed to non-equilibrated initial atomic positions during impingement and the successive relaxations to minimize interfacial energies. The film quality was monitored using Raman spectroscopy and electron microscopy. Based on our experimental results and analyses, it is hypothesized that rearrangements of strained boundary structures during the anneal can lower the interfacial energy change during subsequent growth and produce less stress. Multistep processing was also used to enhance diamond nucleation on Ni. An annealing pretreatment step, that consists of saturating

  8. Properties of true quaternary fission of nuclei with allowance for its multistep and sequential character

    SciTech Connect

    Kadmensky, S. G. Titova, L. V.; Bulychev, A. O.

    2015-07-15

    An analysis of basicmechanisms of binary and ternary fission of nuclei led to the conclusion that true ternary and quaternary fission of nuclei has a sequential two-step (three-step) character, where, at the first step, a fissile nucleus emits a third light particle (third and fourth light particles) under shakeup effects associated with a nonadiabatic character of its collective deformation motion, whereupon the residual nucleus undergoes fission to two fission fragments. Owing to this, the formulas derived earlier for the widths with respect to sequential two- and three-step decays of nuclei in constructing the theory of two-step twoproton decays and multistep decays in chains of genetically related nuclei could be used to describe the relative yields and angular and energy distributions of third and fourth light particles emitted in (α, α), (t, t), and (α, t) pairs upon the true quaternary spontaneous fission of {sup 252}Cf and thermal-neutron-induced fission of {sup 235}U and {sup 233}U target nuclei. Mechanisms that explain a sharp decrease in the yield of particles appearing second in time and entering into the composition of light-particle pairs that originate from true quaternary fission of nuclei in relation to the yields of analogous particles in true ternary fission of nuclei are proposed.

  9. Characterization and Application of Xylene Monooxygenase for Multistep Biocatalysis

    PubMed Central

    Bühler, Bruno; Witholt, Bernard; Hauer, Bernhard; Schmid, Andreas

    2002-01-01

    Xylene monooxygenase of Pseudomonas putida mt-2 catalyzes multistep oxidations of one methyl group of toluene and xylenes. Recombinant Escherichia coli expressing the monooxygenase genes xylM and xylA catalyzes the oxygenation of toluene, pseudocumene, the corresponding alcohols, and the corresponding aldehydes, all by a monooxygenation type of reaction (B. Bühler, A. Schmid, B. Hauer, and B. Witholt, J. Biol. Chem. 275:10085-10092, 2000). Using E. coli expressing xylMA, we investigated the kinetics of this one-enzyme three-step biotransformation. We found that unoxidized substrates like toluene and pseudocumene inhibit the second and third oxygenation steps and that the corresponding alcohols inhibit the third oxygenation step. These inhibitions might promote the energetically more favorable alcohol and aldehyde dehydrogenations in the wild type. Growth of E. coli was strongly affected by low concentrations of pseudocumene and its products. Toxicity and solubility problems were overcome by the use of a two-liquid-phase system with bis(2-ethylhexyl)phthalate as the carrier solvent, allowing high overall substrate and product concentrations. In a fed-batch-based two-liquid-phase process with pseudocumene as the substrate, we observed the consecutive accumulation of aldehyde, acid, and alcohol. Our results indicate that, depending on the reaction conditions, product formation could be directed to one specific product. PMID:11823191

  10. Multistep DBT and regular rational extensions of the isotonic oscillator

    SciTech Connect

    Grandati, Yves

    2012-10-15

    In some recent articles, we developed a new systematic approach to generate solvable rational extensions of primary translationally shape invariant potentials. In this generalized SUSY QM partnership, the DBTs are built on the excited states Riccati-Schroedinger (RS) functions regularized via specific discrete symmetries of the considered potential. In the present paper, we prove that this scheme can be extended in a multistep formulation. Applying this scheme to the isotonic oscillator, we obtain new towers of regular rational extensions of this potential which are strictly isospectral to it. We give explicit expressions for their eigenstates which are associated to the recently discovered exceptional Laguerre polynomials and show explicitly that these extensions inherit the shape invariance properties of the original potential. - Highlights: Black-Right-Pointing-Pointer Hamiltonian hierarchies via SUSY quantum partnership generalized to excited states. Black-Right-Pointing-Pointer Goes beyond the scope of the Crum and Krein-Adler theorems. Black-Right-Pointing-Pointer Complete proofs based on deconjugacy theorems and recurrency scheme. Black-Right-Pointing-Pointer Determinantal expressions for new exceptional Laguerre polynomials. Black-Right-Pointing-Pointer Proof of the hereditary character of the shape invariance.

  11. Statistical properties of multistep enzyme-mediated reactions

    SciTech Connect

    Nemenman, Ilya; Sinitsyn, Nikolai A; De Ronde, Wiet H; Daniels, Bryan C; Mugler, Andrew

    2008-01-01

    Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d/dt (or 'dose-response' curve) and the Fano factor F=variance/ are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.

  12. Optimal spread spectrum watermark embedding via a multistep feasibility formulation.

    PubMed

    Altun, H Oktay; Orsdemir, Adem; Sharma, Gaurav; Bocko, Mark F

    2009-02-01

    We consider optimal formulations of spread spectrum watermark embedding where the common requirements of watermarking, such as perceptual closeness of the watermarked image to the cover and detectability of the watermark in the presence of noise and compression, are posed as constraints while one metric pertaining to these requirements is optimized. We propose an algorithmic framework for solving these optimal embedding problems via a multistep feasibility approach that combines projections onto convex sets (POCS) based feasibility watermarking with a bisection parameter search for determining the optimum value of the objective function and the optimum watermarked image. The framework is general and can handle optimal watermark embedding problems with convex and quasi-convex formulations of watermark requirements with assured convergence to the global optimum. The proposed scheme is a natural extension of set-theoretic watermark design and provides a link between convex feasibility and optimization formulations for watermark embedding. We demonstrate a number of optimal watermark embeddings in the proposed framework corresponding to maximal robustness to additive noise, maximal robustness to compression, minimal frequency weighted perceptual distortion, and minimal watermark texture visibility. Experimental results demonstrate that the framework is effective in optimizing the desired characteristic while meeting the constraints. The results also highlight both anticipated and unanticipated competition between the common requirements for watermark embedding.

  13. Solvent recyclability in a multistep direct liquefaction process

    SciTech Connect

    Hetland, M.D.; Rindt, J.R.

    1995-12-31

    Direct liquefaction research at the Energy & Environmental Research Center (EERC) has, for a number of years, concentrated on developing a direct liquefaction process specifically for low-rank coals (LRCs) through the use of hydrogen-donating solvents and solvents similar to coal-derived liquids, the water/gas shift reaction, and lower-severity reaction conditions. The underlying assumption of all of the research was that advantage could be taken of the reactivity and specific qualities of LRCs to produce a tetrahydrofuran (THF)-soluble material that might be easier to upgrade than the soluble residuum produced during direct liquefaction of high-rank coals. A multistep approach was taken to produce the THF-soluble material, consisting of (1) preconversion treatment to prepare the coal for solubilization, (2) solubilization of the coal in the solvent, and (3) polishing to complete solubilization of the remaining material. The product of these three steps can then be upgraded during a traditional hydrotreatment step. The results of the EERC`s research indicated that additional studies to develop this process more fully were justified. Two areas were targeted for further research: (1) determination of the recyclability of the solvent used during solubilization and (2) determination of the minimum severity required for hydrotreatment of the liquid product. The current project was funded to investigate these two areas.

  14. Multistep hopping and extracellular charge transfer in microbial redox chains.

    PubMed

    Pirbadian, Sahand; El-Naggar, Mohamed Y

    2012-10-28

    Dissimilatory metal-reducing bacteria are microorganisms that gain energy by transferring respiratory electrons to extracellular solid-phase electron acceptors. In addition to its importance for physiology and natural environmental processes, this form of metabolism is being investigated for energy conversion and fuel production in bioelectrochemical systems, where microbes are used as biocatalysts at electrodes. One proposed strategy to accomplish this extracellular charge transfer involves forming a conductive pathway to electrodes by incorporating redox components on outer cell membranes and along extracellular appendages known as microbial nanowires within biofilms. To describe extracellular charge transfer in microbial redox chains, we employed a model based on incoherent hopping between sites in the chain and an interfacial treatment of electrochemical interactions with the surrounding electrodes. Based on this model, we calculated the current-voltage (I-V) characteristics and found the results to be in good agreement with I-V measurements across and along individual microbial nanowires produced by the bacterium Shewanella oneidensis MR-1. Based on our analysis, we propose that multistep hopping in redox chains constitutes a viable strategy for extracellular charge transfer in microbial biofilms.

  15. Comprehensive Control of Networked Control Systems with Multistep Delay

    PubMed Central

    Jiang, Jie

    2014-01-01

    In networked control systems with multi-step delay, long time-delay causes vacant sampling and controller design difficulty. In order to solve the above problems, comprehensive control methods are proposed in this paper. Time-delay compensation control and linear-quadratic-Guassian (LQG) optimal control are adopted and the systems switch different controllers between two different states. LQG optimal controller is used with probability 1 − α in normal state, which is shown to render the systems mean square exponentially stable. Time-delay compensation controller is used with probability α in abnormal state to compensate vacant sampling and long time-delay. In addition, a buffer window is established at the actuator of the systems to store some history control inputs which are used to estimate the control state of present sampling period under the vacant sampling cases. The comprehensive control methods simplify control design which is easier to be implemented in engineering. The performance of the systems is also improved. Simulation results verify the validity of the proposed theory. PMID:25101322

  16. Multistep tumorigenesis of multiple myeloma: its molecular delineation.

    PubMed

    Iida, Shinsuke; Ueda, Ryuzo

    2003-04-01

    Multiple myeloma (MM) is an incurable malignant neoplasm affecting terminally differentiated B-cells. It derives from post-germinal center B-cells and develops as a result of multistep tumorigenic events, because approximately one third of all MM cases have a history of preceding monoclonal gammopathy of undetermined significance (MGUS) or smoldering myeloma. MM terminates in the formation of extramedullary invasion or in secondary plasma cell leukemia. To account for this clinical experience, investigators have found that intrinsic chromosomal instability followed by complex chromosomal translocations/deletions plays a crucial role in the development from MGUS to MM. Representative aberrations include chromosomal rearrangements involving 14q32 loci and deletion at the long arm of chromosome 13. Contributing to the progression of MM itself are genomic instability and altered methylation of the specific gene promoters. The former results in activation of specific oncogenes such as RAS and FGFR3 or in inactivation of p53, and the latter results in inactivation of tumor suppressor genes, including p16. An accurate understanding of each of these molecular events should help clarify the development of specific molecular targeting therapies based on the differences in dysfunctional signaling pathways found in the cells of all MM patients.

  17. Droplet-based microsystem for multi-step bioreactions.

    PubMed

    Wang, Fang; Burns, Mark A

    2010-06-01

    A droplet-based microfluidic platform was used to perform on-chip droplet generation, merging and mixing for applications in multi-step reactions and assays. Submicroliter-sized droplets can be produced separately from three identical droplet-generation channels and merged together in a single chamber. Three different mixing strategies were used for mixing the merged droplet. For pure diffusion, the reagents were mixed in approximately 10 min. Using flow around the stationary droplet to induce circulatory flow within the droplet, the mixing time was decreased to approximately one minute. The shortest mixing time (10 s) was obtained with bidirectional droplet motion between the chamber and channel, and optimization could result in a total time of less than 1 s. We also tested this on-chip droplet generation and manipulation platform using a two-step thermal cycled bioreaction: nested TaqMan PCR. With the same concentration of template DNA, the two-step reaction in a well-mixed merged droplet shows a cycle threshold of approximately 6 cycles earlier than that in the diffusively mixed droplet, and approximately 40 cycles earlier than the droplet-based regular (single-step) TaqMan PCR.

  18. A Multistep Chaotic Model for Municipal Solid Waste Generation Prediction

    PubMed Central

    Song, Jingwei; He, Jiaying

    2014-01-01

    Abstract In this study, a univariate local chaotic model is proposed to make one-step and multistep forecasts for daily municipal solid waste (MSW) generation in Seattle, Washington. For MSW generation prediction with long history data, this forecasting model was created based on a nonlinear dynamic method called phase-space reconstruction. Compared with other nonlinear predictive models, such as artificial neural network (ANN) and partial least square–support vector machine (PLS-SVM), and a commonly used linear seasonal autoregressive integrated moving average (sARIMA) model, this method has demonstrated better prediction accuracy from 1-step ahead prediction to 14-step ahead prediction assessed by both mean absolute percentage error (MAPE) and root mean square error (RMSE). Max error, MAPE, and RMSE show that chaotic models were more reliable than the other three models. As chaotic models do not involve random walk, their performance does not vary while ANN and PLS-SVM make different forecasts in each trial. Moreover, this chaotic model was less time consuming than ANN and PLS-SVM models. PMID:25125942

  19. Automation or De-automation

    NASA Astrophysics Data System (ADS)

    Gorlach, Igor; Wessel, Oliver

    2008-09-01

    In the global automotive industry, for decades, vehicle manufacturers have continually increased the level of automation of production systems in order to be competitive. However, there is a new trend to decrease the level of automation, especially in final car assembly, for reasons of economy and flexibility. In this research, the final car assembly lines at three production sites of Volkswagen are analysed in order to determine the best level of automation for each, in terms of manufacturing costs, productivity, quality and flexibility. The case study is based on the methodology proposed by the Fraunhofer Institute. The results of the analysis indicate that fully automated assembly systems are not necessarily the best option in terms of cost, productivity and quality combined, which is attributed to high complexity of final car assembly systems; some de-automation is therefore recommended. On the other hand, the analysis shows that low automation can result in poor product quality due to reasons related to plant location, such as inadequate workers' skills, motivation, etc. Hence, the automation strategy should be formulated on the basis of analysis of all relevant aspects of the manufacturing process, such as costs, quality, productivity and flexibility in relation to the local context. A more balanced combination of automated and manual assembly operations provides better utilisation of equipment, reduces production costs and improves throughput.

  20. Stability with large step sizes for multistep discretizations of stiff ordinary differential equations

    NASA Technical Reports Server (NTRS)

    Majda, George

    1986-01-01

    One-leg and multistep discretizations of variable-coefficient linear systems of ODEs having both slow and fast time scales are investigated analytically. The stability properties of these discretizations are obtained independent of ODE stiffness and compared. The results of numerical computations are presented in tables, and it is shown that for large step sizes the stability of one-leg methods is better than that of the corresponding linear multistep methods.

  1. Stability with large step sizes for multistep discretizations of stiff ordinary differential equations

    NASA Technical Reports Server (NTRS)

    Majda, George

    1986-01-01

    One-leg and multistep discretizations of variable-coefficient linear systems of ODEs having both slow and fast time scales are investigated analytically. The stability properties of these discretizations are obtained independent of ODE stiffness and compared. The results of numerical computations are presented in tables, and it is shown that for large step sizes the stability of one-leg methods is better than that of the corresponding linear multistep methods.

  2. Genetics

    USDA-ARS?s Scientific Manuscript database

    The genus Capsicum represents one of several well characterized Solanaceous genera. A wealth of classical and molecular genetics research is available for the genus. Information gleaned from its cultivated relatives, tomato and potato, provide further insight for basic and applied studies. Early ...

  3. Genetics

    USDA-ARS?s Scientific Manuscript database

    Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

  4. A new theory for multistep discretizations of stiff ordinary differential equations: Stability with large step sizes

    NASA Technical Reports Server (NTRS)

    Majda, G.

    1985-01-01

    A large set of variable coefficient linear systems of ordinary differential equations which possess two different time scales, a slow one and a fast one is considered. A small parameter epsilon characterizes the stiffness of these systems. A system of o.d.e.s. in this set is approximated by a general class of multistep discretizations which includes both one-leg and linear multistep methods. Sufficient conditions are determined under which each solution of a multistep method is uniformly bounded, with a bound which is independent of the stiffness of the system of o.d.e.s., when the step size resolves the slow time scale, but not the fast one. This property is called stability with large step sizes. The theory presented lets one compare properties of one-leg methods and linear multistep methods when they approximate variable coefficient systems of stiff o.d.e.s. In particular, it is shown that one-leg methods have better stability properties with large step sizes than their linear multistep counter parts. The theory also allows one to relate the concept of D-stability to the usual notions of stability and stability domains and to the propagation of errors for multistep methods which use large step sizes.

  5. Stochastic modeling of biochemical systems with multistep reactions using state-dependent time delay

    PubMed Central

    Wu, Qianqian; Tian, Tianhai

    2016-01-01

    To deal with the growing scale of molecular systems, sophisticated modelling techniques have been designed in recent years to reduce the complexity of mathematical models. Among them, a widely used approach is delayed reaction for simplifying multistep reactions. However, recent research results suggest that a delayed reaction with constant time delay is unable to describe multistep reactions accurately. To address this issue, we propose a novel approach using state-dependent time delay to approximate multistep reactions. We first use stochastic simulations to calculate time delay arising from multistep reactions exactly. Then we design algorithms to calculate time delay based on system dynamics precisely. To demonstrate the power of proposed method, two processes of mRNA degradation are used to investigate the function of time delay in determining system dynamics. In addition, a multistep pathway of metabolic synthesis is used to explore the potential of the proposed method to simplify multistep reactions with nonlinear reaction rates. Simulation results suggest that the state-dependent time delay is a promising and accurate approach to reduce model complexity and decrease the number of unknown parameters in the models. PMID:27553753

  6. Contributions of Dopamine-Related Genes and Environmental Factors to Highly Sensitive Personality: A Multi-Step Neuronal System-Level Approach

    PubMed Central

    Chen, Chunhui; Chen, Chuansheng; Moyzis, Robert; Stern, Hal; He, Qinghua; Li, He; Li, Jin; Zhu, Bi; Dong, Qi

    2011-01-01

    Traditional behavioral genetic studies (e.g., twin, adoption studies) have shown that human personality has moderate to high heritability, but recent molecular behavioral genetic studies have failed to identify quantitative trait loci (QTL) with consistent effects. The current study adopted a multi-step approach (ANOVA followed by multiple regression and permutation) to assess the cumulative effects of multiple QTLs. Using a system-level (dopamine system) genetic approach, we investigated a personality trait deeply rooted in the nervous system (the Highly Sensitive Personality, HSP). 480 healthy Chinese college students were given the HSP scale and genotyped for 98 representative polymorphisms in all major dopamine neurotransmitter genes. In addition, two environment factors (stressful life events and parental warmth) that have been implicated for their contributions to personality development were included to investigate their relative contributions as compared to genetic factors. In Step 1, using ANOVA, we identified 10 polymorphisms that made statistically significant contributions to HSP. In Step 2, these polymorphism's main effects and interactions were assessed using multiple regression. This model accounted for 15% of the variance of HSP (p<0.001). Recent stressful life events accounted for an additional 2% of the variance. Finally, permutation analyses ascertained the probability of obtaining these findings by chance to be very low, p ranging from 0.001 to 0.006. Dividing these loci by the subsystems of dopamine synthesis, degradation/transport, receptor and modulation, we found that the modulation and receptor subsystems made the most significant contribution to HSP. The results of this study demonstrate the utility of a multi-step neuronal system-level approach in assessing genetic contributions to individual differences in human behavior. It can potentially bridge the gap between the high heritability estimates based on traditional behavioral genetics

  7. Automation pilot

    NASA Technical Reports Server (NTRS)

    1983-01-01

    An important concept of the Action Information Management System (AIMS) approach is to evaluate office automation technology in the context of hands on use by technical program managers in the conduct of human acceptance difficulties which may accompany the transition to a significantly changing work environment. The improved productivity and communications which result from application of office automation technology are already well established for general office environments, but benefits unique to NASA are anticipated and these will be explored in detail.

  8. Automated liquid operation method for microfluidic heterogeneous immunoassay.

    PubMed

    Yi, Hui; Pan, Jian-Zhang; Shi, Xiao-Tong; Fang, Qun

    2013-02-15

    In this work, an automated liquid operation method for multistep heterogeneous immunoassay toward point of care testing (POCT) was proposed. A miniaturized peristaltic pump was developed to control the flow direction, flow time and flow rate in the microliter range according to a program. The peristaltic pump has the advantages of simple structure, small size, low cost, and easy to build and use. By coupling the peristaltic pump with an antibody-coated capillary and a reagent-preloaded cartridge, the complicated liquid handling operation for heterogeneous immunoassay, including sample metering and introduction, multistep reagent introduction and rinsing, could be triggered by an action and accomplished automatically in 12 min. The analytical performance of the present immunoassay system was demonstrated in the measurement of human IgG with fluorescence detection. A detection limit of 0.68 μg/mL IgG and a dynamic range of 2-300 μg/mL were obtained.

  9. Office automation.

    PubMed

    Arenson, R L

    1986-03-01

    By now, the term "office automation" should have more meaning for those readers who are not intimately familiar with the subject. Not all of the preceding material pertains to every department or practice, but certainly, word processing and simple telephone management are key items. The size and complexity of the organization will dictate the usefulness of electronic mail and calendar management, and the individual radiologist's personal needs and habits will determine the usefulness of the home computer. Perhaps the most important ingredient for success in the office automation arena relates to the ability to integrate information from various systems in a simple and flexible manner. Unfortunately, this is perhaps the one area that most office automation systems have ignored or handled poorly. In the personal computer world, there has been much emphasis recently on integration of packages such as spreadsheet, database management, word processing, graphics, time management, and communications. This same philosophy of integration has been applied to a few office automation systems, but these are generally vendor-specific and do not allow for a mixture of foreign subsystems. During the next few years, it is likely that a few vendors will emerge as dominant in this integrated office automation field and will stress simplicity and flexibility as major components.

  10. Multistep process of squamous differentiation in tracheobronchial epithelial cells in vitro: analogy with epidermal differentiation.

    PubMed Central

    Jetten, A M

    1989-01-01

    The lung, in particular the bronchial epithelium, is a major site for tumor formation in humans. Environmental factors, such as cigarette smoke, in conjunction with genetic factors are important determinants in this disease. Malignant cells exhibit alterations in their control of proliferation and differentiation. It is believed that the acquisition of defects in the regulation of these processes is important in the process of carcinogenesis. A clear insight into the basic mechanisms of the regulation of proliferation and differentiation is required to understand the molecular mechanisms involved in tumor development and in other pathological conditions. Studies using in vitro cell culture systems of tracheobronchial epithelial cells provide useful models in which to study the regulation of differentiation and proliferation. The clonogenic cells derived from the treacheobronchial epithelium are pluripotent: They have self-renewal capacity and can differentiate along either a normal, mucosecretory, or a squamous cell pathway. Squamous differentiation in tracheobronchial epithelial cells has many morphological, biochemical, and regulatory properties in common with epidermal differentiation. This pathway of differentiation is a multistep process consisting of at least three stages. In the initial stage, cells become committed to terminal cell division. This is followed by the expression of the squamous differentiated phenotype and finally cornification. Various factors, such as several growth factors, retinoids, calcium ions, and phorbol esters, regulate the program of differentiation at different stages. Studies have indicated that the controls of proliferation and differentiation are interrelated. Cell lines established from tracheobronchial epithelial cells expressing SV 40 large T-antigen, as well as carcinoma cell lines, exhibit altered responses to growth and differentiation regulatory factors. Alterations in the commitment to terminal cell division must be a

  11. Comprehensive Glycomics of a Multistep Human Brain Tumor Model Reveals Specific Glycosylation Patterns Related to Malignancy.

    PubMed

    Furukawa, Jun-ichi; Tsuda, Masumi; Okada, Kazue; Kimura, Taichi; Piao, Jinhua; Tanaka, Shinya; Shinohara, Yasuro

    2015-01-01

    Cancer cells frequently express glycans at different levels and/or with fundamentally different structures from those expressed by normal cells, and therefore elucidation and manipulation of these glycosylations may provide a beneficial approach to cancer therapy. However, the relationship between altered glycosylation and causal genetic alteration(s) is only partially understood. Here, we employed a unique approach that applies comprehensive glycomic analysis to a previously described multistep tumorigenesis model. Normal human astrocytes were transformed via the serial introduction of hTERT, SV40ER, H-RasV12, and myrAKT, thereby mimicking human brain tumor grades I-IV. More than 160 glycans derived from three major classes of cell surface glycoconjugates (N- and O-glycans on glycoproteins, and glycosphingolipids) were quantitatively explored, and specific glycosylation patterns related to malignancy were systematically identified. The sequential introduction of hTERT, SV40ER, H-RasV12, and myrAKT led to (i) temporal expression of pauci-mannose/mono-antennary type N-glycans and GD3 (hTERT); (ii) switching from ganglio- to globo-series glycosphingolipids and the appearance of Neu5Gc (hTERT and SV40ER); (iii) temporal expression of bisecting GlcNAc residues, α2,6-sialylation, and stage-specific embryonic antigen-4, accompanied by suppression of core 2 O-glycan biosynthesis (hTERT, SV40ER and Ras); and (iv) increased expression of (neo)lacto-series glycosphingolipids and fucosylated N-glycans (hTERT, SV40ER, Ras and AKT). These sequential and transient glycomic alterations may be useful for tumor grade diagnosis and tumor prognosis, and also for the prediction of treatment response.

  12. Habitat automation

    NASA Technical Reports Server (NTRS)

    Swab, Rodney E.

    1992-01-01

    A habitat, on either the surface of the Moon or Mars, will be designed and built with the proven technologies of that day. These technologies will be mature and readily available to the habitat designer. We believe an acceleration of the normal pace of automation would allow a habitat to be safer and more easily maintained than would be the case otherwise. This document examines the operation of a habitat and describes elements of that operation which may benefit from an increased use of automation. Research topics within the automation realm are then defined and discussed with respect to the role they can have in the design of the habitat. Problems associated with the integration of advanced technologies into real-world projects at NASA are also addressed.

  13. Direct observation of multistep energy transfer in LHCII with fifth-order 3D electronic spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Zhengyang; Lambrev, Petar H.; Wells, Kym L.; Garab, Győző; Tan, Howe-Siang

    2015-07-01

    During photosynthesis, sunlight is efficiently captured by light-harvesting complexes, and the excitation energy is then funneled towards the reaction centre. These photosynthetic excitation energy transfer (EET) pathways are complex and proceed in a multistep fashion. Ultrafast two-dimensional electronic spectroscopy (2DES) is an important tool to study EET processes in photosynthetic complexes. However, the multistep EET processes can only be indirectly inferred by correlating different cross peaks from a series of 2DES spectra. Here we directly observe multistep EET processes in LHCII using ultrafast fifth-order three-dimensional electronic spectroscopy (3DES). We measure cross peaks in 3DES spectra of LHCII that directly indicate energy transfer from excitons in the chlorophyll b (Chl b) manifold to the low-energy level chlorophyll a (Chl a) via mid-level Chl a energy states. This new spectroscopic technique allows scientists to move a step towards mapping the complete complex EET processes in photosynthetic systems.

  14. Direct observation of multistep energy transfer in LHCII with fifth-order 3D electronic spectroscopy

    PubMed Central

    Zhang, Zhengyang; Lambrev, Petar H.; Wells, Kym L.; Garab, Győző; Tan, Howe-Siang

    2015-01-01

    During photosynthesis, sunlight is efficiently captured by light-harvesting complexes, and the excitation energy is then funneled towards the reaction centre. These photosynthetic excitation energy transfer (EET) pathways are complex and proceed in a multistep fashion. Ultrafast two-dimensional electronic spectroscopy (2DES) is an important tool to study EET processes in photosynthetic complexes. However, the multistep EET processes can only be indirectly inferred by correlating different cross peaks from a series of 2DES spectra. Here we directly observe multistep EET processes in LHCII using ultrafast fifth-order three-dimensional electronic spectroscopy (3DES). We measure cross peaks in 3DES spectra of LHCII that directly indicate energy transfer from excitons in the chlorophyll b (Chl b) manifold to the low-energy level chlorophyll a (Chl a) via mid-level Chl a energy states. This new spectroscopic technique allows scientists to move a step towards mapping the complete complex EET processes in photosynthetic systems. PMID:26228055

  15. Modeling the Auto-Ignition of Biodiesel Blends with a Multi-Step Model

    SciTech Connect

    Toulson, Dr. Elisa; Allen, Casey M; Miller, Dennis J; McFarlane, Joanna; Schock, Harold; Lee, Tonghun

    2011-01-01

    There is growing interest in using biodiesel in place of or in blends with petrodiesel in diesel engines; however, biodiesel oxidation chemistry is complicated to directly model and existing surrogate kinetic models are very large, making them computationally expensive. The present study describes a method for predicting the ignition behavior of blends of n-heptane and methyl butanoate, fuels whose blends have been used in the past as a surrogate for biodiesel. The autoignition is predicted using a multistep (8-step) model in order to reduce computational time and make this a viable tool for implementation into engine simulation codes. A detailed reaction mechanism for n-heptane-methyl butanoate blends was used as a basis for validating the multistep model results. The ignition delay trends predicted by the multistep model for the n-heptane-methyl butanoate blends matched well with that of the detailed CHEMKIN model for the majority of conditions tested.

  16. Automating Finance

    ERIC Educational Resources Information Center

    Moore, John

    2007-01-01

    In past years, higher education's financial management side has been riddled with manual processes and aging mainframe applications. This article discusses schools which had taken advantage of an array of technologies that automate billing, payment processing, and refund processing in the case of overpayment. The investments are well worth it:…

  17. Maintaining canine sperm function and osmolyte content with multistep freezing protocol and different cryoprotective agents.

    PubMed

    Setyawan, Erif Maha Nugraha; Kim, Min Jung; Oh, Hyun Ju; Kim, Geon A; Jo, Young Kwang; Lee, Seok Hee; Choi, Yoo Bin; Lee, Byeong Chun

    2015-10-01

    Cryopreservation procedures cause osmotic stress to spermatozoa following cryoinjury and reduce their content of osmolytes. Conventional method for cryoprotectant loading and dilution on canine semen freezing which could be categorized in single step protocol, makes decreasing in sperm performance such as motility, morphology and viability. Therefore, the objective of the present study was to determine if a multistep protocol using glycerol or ethylene glycol can be used to overcome the osmotic sensitivity of canine spermatozoa, and to identify osmolytes that were involved in regulation of osmotic stress. A multistep protocol, comprising serial loading and dilution of cryoprotective agents by dividing the total volume of extender into 4 steps (14%, 19%, 27%, and 40%) every 30s, was compared to a single step method. Frozen-thawed spermatozoa in the multistep group showed superior quality (P<0.05) compared with the single step process in progressive motility (23.3 ± 1.3% vs. 12.5 ± 1.6%), intact membranes (66.5 ± 2.8% vs. 49.5 ± 2.6%) and bent tail (29.2 ± 3.2% vs. 46.2 ± 1.9%). Multistep also succeeded in minimizing loss of the osmolytes carnitine (20.6 ± 2.0 nmol/U G6PDH vs. 10.8 ± 2.1 nmol/U G6PDH) and glutamate (18.4 ± 1.6 nmol/U G6PDH vs. 14.4 ± 0.8 nmol/U G6PDH) compared to the single step group. Moreover, glycerol with multistep was more advantageous for maintaining sperm quality than ethylene glycol. In conclusion, the multistep protocol with glycerol can be used to improve the morphology, motility and osmolytes content of frozen-thawed canine spermatozoa. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. On the origin of multi-step spin transition behaviour in 1D nanoparticles

    NASA Astrophysics Data System (ADS)

    Chiruta, Daniel; Jureschi, Catalin-Maricel; Linares, Jorge; Dahoo, Pierre Richard; Garcia, Yann; Rotaru, Aurelian

    2015-09-01

    To investigate the spin state switching mechanism in spin crossover (SCO) nanoparticles, a special attention is given to three-step thermally induced SCO behavior in 1D chains. An additional term is included in the standard Ising-like Hamiltonian to account for the border interaction between SCO molecules and its local environment. It is shown that this additional interaction, together with the short range interaction, drives the multi-steps thermal hysteretic behavior in 1D SCO systems. The relation between a polymeric matrix and this particular multi-step SCO phenomenon is discussed accordingly. Finally, the environmental influence on the SCO system's size is analyzed as well.

  19. Surface Modified Particles By Multi-Step Addition And Process For The Preparation Thereof

    DOEpatents

    Cook, Ronald Lee; Elliott, Brian John; Luebben, Silvia DeVito; Myers, Andrew William; Smith, Bryan Matthew

    2006-01-17

    The present invention relates to a new class of surface modified particles and to a multi-step surface modification process for the preparation of the same. The multi-step surface functionalization process involves two or more reactions to produce particles that are compatible with various host systems and/or to provide the particles with particular chemical reactivities. The initial step comprises the attachment of a small organic compound to the surface of the inorganic particle. The subsequent steps attach additional compounds to the previously attached organic compounds through organic linking groups.

  20. A Multistep Synthesis Featuring Classic Carbonyl Chemistry for the Advanced Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Duff, David B.; Abbe, Tyler G.; Goess, Brian C.

    2012-01-01

    A multistep synthesis of 5-isopropyl-1,3-cyclohexanedione is carried out from three commodity chemicals. The sequence involves an aldol condensation, Dieckmann-type annulation, ester hydrolysis, and decarboxylation. No purification is required until after the final step, at which point gravity column chromatography provides the desired product in…

  1. A Multistep Synthesis Incorporating a Green Bromination of an Aromatic Ring

    ERIC Educational Resources Information Center

    Cardinal, Pascal; Greer, Brandon; Luong, Horace; Tyagunova, Yevgeniya

    2012-01-01

    Electrophilic aromatic substitution is a fundamental topic taught in the undergraduate organic chemistry curriculum. A multistep synthesis that includes a safer and greener method for the bromination of an aromatic ring than traditional bromination methods is described. This experiment is multifaceted and can be used to teach students about…

  2. Experimental study on multi-step creep properties of rat skins.

    PubMed

    Chen, Gang; Cui, Shibo; You, Lin; Li, Yan; Mei, Yun-Hui; Chen, Xu

    2015-06-01

    Tension, single-step creep, and multi-step creep of rat skins at room temperature were experimentally studied. We studied the effects of loading histories of high stress creep, low stress creep, and stress relaxation on multi-step creep. Microstructure of rat skins after prescribed tests were observed microscopically with the help of standard hematoxylin and eosin (H&E). The void ratios were also analyzed. The loading histories of high stress creep, low stress creep, and stress relaxation have significant influence on multi-step creep. We found that the creep strain and its rate in the steady-state stage and the creep-fatigue life of rat skins are sensitive to creep stress. Low stress creep after the loading history of high stress creep is characterized as a recovery of strain and a zero strain rate. Both the loading history of low stress creep and stress relaxation act as a recovery in multi-step creep, and they are driven by a same mechanism in the creep strain and the void ratio of rat skins. The loading history, of which sequence is as followings successively: low stress creep, stress relaxation, and high stress creep, helps to obtain the largest creep strain at the lowest void ratio. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Two-dimensional Paper‡ Networks: programmable fluidic disconnects for multi-step processes in shaped paper

    PubMed Central

    Trinh, Philip; Ball, Cameron; Fu, Elain; Yager, Paul

    2016-01-01

    Most laboratory assays take advantage of multi-step protocols to achieve high performance, but conventional paper-based tests (e.g., lateral flow tests) are generally limited to assays that can be carried out in a single fluidic step. We have developed two-dimensional paper networks (2DPNs) that use materials from lateral flow tests but reconfigure them to enable programming of multi-step reagent delivery sequences. The 2DPN uses multiple converging fluid inlets to control the arrival time of each fluid to a detection zone or reaction zone, and it requires a method to disconnect each fluid source in a corresponding timed sequence. Here, we present a method that allows programmed disconnection of fluid sources required for multi-step delivery. A 2DPN with legs of different lengths is inserted into a shared buffer well, and the dropping fluid surface disconnects each leg at in a programmable sequence. This approach could enable multi-step laboratory assays to be converted into simple point-of-care devices that have high performance yet remain easy to use. PMID:22037591

  4. A novel high breakdown voltage lateral bipolar transistor on SOI with multizone doping and multistep oxide

    NASA Astrophysics Data System (ADS)

    Loan, Sajad A.; Qureshi, S.; Iyer, S. S. Kumar

    2009-02-01

    A novel high breakdown voltage lateral bipolar junction transistor (LBJT) on silicon-on- insulator (SOI) is proposed. The novelty of the device is the use of the combination of multistep-doped drift region and multistep buried oxide. The steps in doping and in oxide thickness have been used as a replacement for much complex linearly varying drift doping and linearly varying oxide thickness. The LBJT structure incorporating the combination of multistep doping and multistep oxide is analyzed for electrical characteristics using a two-dimensional numerical simulator MEDICI. Numerical simulation has demonstrated that the breakdown voltage of the proposed device with a two-zone step doped (TZSD) drift region is >150% higher than the conventional device. It has been observed that increasing the number of doping zones to 3 from 2 results in a >40% rise in breakdown voltage. The proposed device gives high breakdown voltage even at high doping concentration in the collector drift region. This reduces the on-resistance of the device and thus improves its speed. The dependence of breakdown voltage on various device parameters has been extensively studied to achieve optimum device performance. A process flow for the device fabrication is also being proposed.

  5. Use of Chiral Oxazolidinones for a Multi-Step Synthetic Laboratory Module

    ERIC Educational Resources Information Center

    Betush, Matthew P.; Murphree, S. Shaun

    2009-01-01

    Chiral oxazolidinone chemistry is used as a framework for an advanced multi-step synthesis lab. The cost-effective and robust preparation of chiral starting materials is presented, as well as the use of chiral auxiliaries in a synthesis scheme that is appropriate for students currently in the second semester of the organic sequence. (Contains 1…

  6. Attention and Multistep Problem Solving in 24-Month-Old Children

    ERIC Educational Resources Information Center

    Carrico, Renee L.

    2013-01-01

    The current study examined the role of increased attentional load in 24 month-old children's multistep problem-solving behavior. Children solved an object-based nonspatial working-memory search task, to which a motor component of varying difficulty was added. Significant disruptions in search performance were observed with the introduction of the…

  7. A Bias and Variance Analysis for Multistep-Ahead Time Series Forecasting.

    PubMed

    Ben Taieb, Souhaib; Atiya, Amir F

    2016-01-01

    Multistep-ahead forecasts can either be produced recursively by iterating a one-step-ahead time series model or directly by estimating a separate model for each forecast horizon. In addition, there are other strategies; some of them combine aspects of both aforementioned concepts. In this paper, we present a comprehensive investigation into the bias and variance behavior of multistep-ahead forecasting strategies. We provide a detailed review of the different multistep-ahead strategies. Subsequently, we perform a theoretical study that derives the bias and variance for a number of forecasting strategies. Finally, we conduct a Monte Carlo experimental study that compares and evaluates the bias and variance performance of the different strategies. From the theoretical and the simulation studies, we analyze the effect of different factors, such as the forecast horizon and the time series length, on the bias and variance components, and on the different multistep-ahead strategies. Several lessons are learned, and recommendations are given concerning the advantages, disadvantages, and best conditions of use of each strategy.

  8. Collaborative Activities for Solving Multi-Step Problems in General Chemistry

    ERIC Educational Resources Information Center

    Tortajada-Genaro, Luis Antonio

    2014-01-01

    The learning of solving multi-step problems is a relevant aim in chemical education for engineering students. In these questions, after analyzing initial data, a complex reasoning and an elaborated mathematical procedure is needed to achieve the correct numerical answer. However, many students are able to effectively use algorithms even with a…

  9. Controlled growth of silica-titania hybrid functional nanoparticles through a multistep microfluidic approach.

    PubMed

    Shiba, K; Sugiyama, T; Takei, T; Yoshikawa, G

    2015-11-11

    Silica/titania-based functional nanoparticles were prepared through controlled nucleation of titania and subsequent encapsulation by silica through a multistep microfluidic approach, which was successfully applied to obtaining aminopropyl-functionalized silica/titania nanoparticles for a highly sensitive humidity sensor.

  10. Multi-step routes of capuchin monkeys in a laser pointer traveling salesman task.

    PubMed

    Howard, Allison M; Fragaszy, Dorothy M

    2014-09-01

    Prior studies have claimed that nonhuman primates plan their routes multiple steps in advance. However, a recent reexamination of multi-step route planning in nonhuman primates indicated that there is no evidence for planning more than one step ahead. We tested multi-step route planning in capuchin monkeys using a pointing device to "travel" to distal targets while stationary. This device enabled us to determine whether capuchins distinguish the spatial relationship between goals and themselves and spatial relationships between goals and the laser dot, allocentrically. In Experiment 1, two subjects were presented with identical food items in Near-Far (one item nearer to subject) and Equidistant (both items equidistant from subject) conditions with a laser dot visible between the items. Subjects moved the laser dot to the items using a joystick. In the Near-Far condition, one subject demonstrated a bias for items closest to self but the other subject chose efficiently. In the second experiment, subjects retrieved three food items in similar Near-Far and Equidistant arrangements. Both subjects preferred food items nearest the laser dot and showed no evidence of multi-step route planning. We conclude that these capuchins do not make choices on the basis of multi-step look ahead strategies.

  11. A Multistep Synthesis Incorporating a Green Bromination of an Aromatic Ring

    ERIC Educational Resources Information Center

    Cardinal, Pascal; Greer, Brandon; Luong, Horace; Tyagunova, Yevgeniya

    2012-01-01

    Electrophilic aromatic substitution is a fundamental topic taught in the undergraduate organic chemistry curriculum. A multistep synthesis that includes a safer and greener method for the bromination of an aromatic ring than traditional bromination methods is described. This experiment is multifaceted and can be used to teach students about…

  12. Use of Chiral Oxazolidinones for a Multi-Step Synthetic Laboratory Module

    ERIC Educational Resources Information Center

    Betush, Matthew P.; Murphree, S. Shaun

    2009-01-01

    Chiral oxazolidinone chemistry is used as a framework for an advanced multi-step synthesis lab. The cost-effective and robust preparation of chiral starting materials is presented, as well as the use of chiral auxiliaries in a synthesis scheme that is appropriate for students currently in the second semester of the organic sequence. (Contains 1…

  13. Multistep Synthesis of a Terphenyl Derivative Showcasing the Diels-Alder Reaction

    ERIC Educational Resources Information Center

    Davie, Elizabeth A. Colby

    2015-01-01

    An adaptable multistep synthesis project designed for the culmination of a second-year organic chemistry laboratory course is described. The target compound is a terphenyl derivative that is an intermediate in the synthesis of compounds used in organic light-emitting devices. Students react a conjugated diene with dimethylacetylene dicarboxylate…

  14. Biocatalyzed Regioselective Synthesis in Undergraduate Organic Laboratories: Multistep Synthesis of 2-Arachidonoylglycerol

    ERIC Educational Resources Information Center

    Johnston, Meghan R.; Makriyannis, Alexandros; Whitten, Kyle M.; Drew, Olivia C.; Best, Fiona A.

    2016-01-01

    In order to introduce the concepts of biocatalysis and its utility in synthesis to organic chemistry students, a multistep synthesis of endogenous cannabinergic ligand 2-arachidonoylglycerol (2-AG) was tailored for use as a laboratory exercise. Over four weeks, students successfully produced 2-AG, purifying and characterizing products at each…

  15. Attention and Multistep Problem Solving in 24-Month-Old Children

    ERIC Educational Resources Information Center

    Carrico, Renee L.

    2013-01-01

    The current study examined the role of increased attentional load in 24 month-old children's multistep problem-solving behavior. Children solved an object-based nonspatial working-memory search task, to which a motor component of varying difficulty was added. Significant disruptions in search performance were observed with the introduction of the…

  16. A Multistep Synthesis Featuring Classic Carbonyl Chemistry for the Advanced Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Duff, David B.; Abbe, Tyler G.; Goess, Brian C.

    2012-01-01

    A multistep synthesis of 5-isopropyl-1,3-cyclohexanedione is carried out from three commodity chemicals. The sequence involves an aldol condensation, Dieckmann-type annulation, ester hydrolysis, and decarboxylation. No purification is required until after the final step, at which point gravity column chromatography provides the desired product in…

  17. Multistep Synthesis of a Terphenyl Derivative Showcasing the Diels-Alder Reaction

    ERIC Educational Resources Information Center

    Davie, Elizabeth A. Colby

    2015-01-01

    An adaptable multistep synthesis project designed for the culmination of a second-year organic chemistry laboratory course is described. The target compound is a terphenyl derivative that is an intermediate in the synthesis of compounds used in organic light-emitting devices. Students react a conjugated diene with dimethylacetylene dicarboxylate…

  18. Biocatalyzed Regioselective Synthesis in Undergraduate Organic Laboratories: Multistep Synthesis of 2-Arachidonoylglycerol

    ERIC Educational Resources Information Center

    Johnston, Meghan R.; Makriyannis, Alexandros; Whitten, Kyle M.; Drew, Olivia C.; Best, Fiona A.

    2016-01-01

    In order to introduce the concepts of biocatalysis and its utility in synthesis to organic chemistry students, a multistep synthesis of endogenous cannabinergic ligand 2-arachidonoylglycerol (2-AG) was tailored for use as a laboratory exercise. Over four weeks, students successfully produced 2-AG, purifying and characterizing products at each…

  19. Mechanical and Metallurgical Evolution of Stainless Steel 321 in a Multi-step Forming Process

    NASA Astrophysics Data System (ADS)

    Anderson, M.; Bridier, F.; Gholipour, J.; Jahazi, M.; Wanjara, P.; Bocher, P.; Savoie, J.

    2016-04-01

    This paper examines the metallurgical evolution of AISI Stainless Steel 321 (SS 321) during multi-step forming, a process that involves cycles of deformation with intermediate heat treatment steps. The multi-step forming process was simulated by implementing interrupted uniaxial tensile testing experiments. Evolution of the mechanical properties as well as the microstructural features, such as twins and textures of the austenite and martensite phases, was studied as a function of the multi-step forming process. The characteristics of the Strain-Induced Martensite (SIM) were also documented for each deformation step and intermediate stress relief heat treatment. The results indicated that the intermediate heat treatments considerably increased the formability of SS 321. Texture analysis showed that the effect of the intermediate heat treatment on the austenite was minor and led to partial recrystallization, while deformation was observed to reinforce the crystallographic texture of austenite. For the SIM, an Olson-Cohen equation type was identified to analytically predict its formation during the multi-step forming process. The generated SIM was textured and weakened with increasing deformation.

  20. Design Automation in Synthetic Biology.

    PubMed

    Appleton, Evan; Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas

    2017-04-03

    Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks.

  1. Production of the cannibalism toxin SDP is a multistep process that requires SdpA and SdpB.

    PubMed

    Pérez Morales, Tiara G; Ho, Theresa D; Liu, Wei-Ting; Dorrestein, Pieter C; Ellermeier, Craig D

    2013-07-01

    During the early stages of sporulation, a subpopulation of Bacillus subtilis cells secrete toxins that kill their genetically identical siblings in a process termed cannibalism. One of these toxins is encoded by the sdpC gene of the sdpABC operon. The active form of the SDP toxin is a 42-amino-acid peptide with a disulfide bond which is processed from an internal fragment of pro-SdpC. The factors required for the processing of pro-SdpC into mature SDP are not known. We provide evidence that pro-SdpC is secreted via the general secretory pathway and that signal peptide cleavage is a required step in the production of SDP. We also demonstrate that SdpAB are essential to produce mature SDP, which has toxin activity. Our data indicate that SdpAB are not required for secretion, translation, or stability of SdpC. Thus, SdpAB may participate in a posttranslation step in the production of SDP. The mature form of the SDP toxin contains a disulfide bond. Our data indicate that while the disulfide bond does increase activity of SDP, it is not essential for SDP activity. We demonstrate that the disulfide bond is formed independently of SdpAB. Taken together, our data suggest that SDP production is a multistep process and that SdpAB are required for SDP production likely by controlling, directly or indirectly, cleavage of SDP from the pro-SdpC precursor.

  2. Automated Sampling Procedures Supported by High Persistence of Bacterial Fecal Indicators and Bacteroidetes Genetic Microbial Source Tracking Markers in Municipal Wastewater during Short-Term Storage at 5°C

    PubMed Central

    Mayer, R. E.; Vierheilig, J.; Egle, L.; Reischer, G. H.; Saracevic, E.; Mach, R. L.; Kirschner, A. K. T.; Zessner, M.; Farnleitner, A. H.

    2015-01-01

    Because of high diurnal water quality fluctuations in raw municipal wastewater, the use of proportional autosampling over a period of 24 h at municipal wastewater treatment plants (WWTPs) to evaluate carbon, nitrogen, and phosphorus removal has become a standard in many countries. Microbial removal or load estimation at municipal WWTPs, however, is still based on manually recovered grab samples. The goal of this study was to establish basic knowledge regarding the persistence of standard bacterial fecal indicators and Bacteroidetes genetic microbial source tracking markers in municipal wastewater in order to evaluate their suitability for automated sampling, as the potential lack of persistence is the main argument against such procedures. Raw and secondary treated wastewater of municipal origin from representative and well-characterized biological WWTPs without disinfection (organic carbon and nutrient removal) was investigated in microcosm experiments at 5 and 21°C with a total storage time of 32 h (including a 24-h autosampling component and an 8-h postsampling phase). Vegetative Escherichia coli and enterococci, as well as Clostridium perfringens spores, were selected as indicators for cultivation-based standard enumeration. Molecular analysis focused on total (AllBac) and human-associated genetic Bacteroidetes (BacHum-UCD, HF183 TaqMan) markers by using quantitative PCR, as well as 16S rRNA gene-based next-generation sequencing. The microbial parameters showed high persistence in both raw and treated wastewater at 5°C under the storage conditions used. Surprisingly, and in contrast to results obtained with treated wastewater, persistence of the microbial markers in raw wastewater was also high at 21°C. On the basis of our results, 24-h autosampling procedures with 5°C storage conditions can be recommended for the investigation of fecal indicators or Bacteroidetes genetic markers at municipal WWTPs. Such autosampling procedures will contribute to better

  3. Multistep integration formulas for the numerical integration of the satellite problem

    NASA Technical Reports Server (NTRS)

    Lundberg, J. B.; Tapley, B. D.

    1981-01-01

    The use of two Class 2/fixed mesh/fixed order/multistep integration packages of the PECE type for the numerical integration of the second order, nonlinear, ordinary differential equation of the satellite orbit problem. These two methods are referred to as the general and the second sum formulations. The derivation of the basic equations which characterize each formulation and the role of the basic equations in the PECE algorithm are discussed. Possible starting procedures are examined which may be used to supply the initial set of values required by the fixed mesh/multistep integrators. The results of the general and second sum integrators are compared to the results of various fixed step and variable step integrators.

  4. Multistep impregnation method for incorporation of high amount of titania into SBA-15

    SciTech Connect

    Wang Wei; Song Mo . E-mail: m.song@lboro.ac.uk

    2006-02-02

    A multistep impregnation method was employed to incorporate high amount of titania into the mesoporous SBA-15 silica. No damage to the SBA-15 silica mesostructures was caused by the loading of titania in every cycle. The existence of titania small nanodomains were confirmed to be present by Raman spectra and UV-vis DRS measurements. High dispersion of them was realized via this method according to the results of low-angle X-ray powder diffraction (XRD), transmission electron microscopy (TEM) and N{sub 2} sorption measurements. Importantly, no blockage of mesostructures was acknowledged with titania content up to 24.4 wt.%. In comparison, normally used one-step impregnation method led to serious blockage of mesopores as the results of formation of bulk titania particles in the mesochannels. Photo-activity test for the removal of oestrogen showed the superiority of the materials synthesized by multistep impregnation method to one-step impregnation method.

  5. Teaching multi-step math skills to adults with disabilities via video prompting.

    PubMed

    Kellems, Ryan O; Frandsen, Kaitlyn; Hansen, Blake; Gabrielsen, Terisa; Clarke, Brynn; Simons, Kalee; Clements, Kyle

    2016-11-01

    The purpose of this study was to evaluate the effectiveness of teaching multi-step math skills to nine adults with disabilities in an 18-21 post-high school transition program using a video prompting intervention package. The dependent variable was the percentage of steps completed correctly. The independent variable was the video prompting intervention, which involved several multi-step math calculation skills: (a) calculating a tip (15%), (b) calculating item unit prices, and (c) adjusting a recipe for more or fewer people. Results indicated a functional relationship between the video prompting interventions and prompting package and the percentage of steps completed correctly. 8 out of the 9 adults showed significant gains immediately after receiving the video prompting intervention.

  6. Color-Tunable Resonant Photoluminescence and Cavity-Mediated Multistep Energy Transfer Cascade.

    PubMed

    Okada, Daichi; Nakamura, Takashi; Braam, Daniel; Dao, Thang Duy; Ishii, Satoshi; Nagao, Tadaaki; Lorke, Axel; Nabeshima, Tatsuya; Yamamoto, Yohei

    2016-07-26

    Color-tunable resonant photoluminescence (PL) was attained from polystyrene microspheres doped with a single polymorphic fluorescent dye, boron-dipyrrin (BODIPY) 1. The color of the resonant PL depends on the assembling morphology of 1 in the microspheres, which can be selectively controlled from green to red by the initial concentration of 1 in the preparation process of the microspheres. Studies on intersphere PL propagation with multicoupled microspheres, prepared by micromanipulation technique, revealed that multistep photon transfer takes place through the microspheres, accompanying energy transfer cascade with stepwise PL color change. The intersphere energy transfer cascade is direction selective, where energy donor-to-acceptor down conversion direction is only allowed. Such cavity-mediated long-distance and multistep energy transfer will be advantageous for polymer photonics device application.

  7. Multi-step wrought processing of TiAl-based alloys

    SciTech Connect

    Fuchs, G.E.

    1997-04-01

    Wrought processing will likely be needed for fabrication of a variety of TiAl-based alloy structural components. Laboratory and development work has usually relied on one-step forging to produce test material. Attempts to scale-up TiAl-based alloy processing has indicated that multi-step wrought processing is necessary. The purpose of this study was to examine potential multi-step processing routes, such as two-step isothermal forging and extrusion + isothermal forging. The effects of processing (I/M versus P/M), intermediate recrystallization heat treatments and processing route on the tensile and creep properties of Ti-48Al-2Nb-2Cr alloys were examined. The results of the testing were then compared to samples from the same heats of materials processed by one-step routes. Finally, by evaluating the effect of processing on microstructure and properties, optimized and potentially lower cost processing routes could be identified.

  8. Using motor milestones as a multistep process to screen preterm infants for cerebral palsy.

    PubMed

    Allen, M C; Alexander, G R

    1997-01-01

    Pediatricians often informally use motor milestones to screen infant motor development, and one advantage is that they can be used during sequential office visits, as a multistep screening process. In this study we evaluated six motor milestones (roll prone to supine, roll supine to prone, sit with support, sit without support, crawl and cruise) as a multistep process in screening for cerebral palsy in 173 high-risk preterm infants (<33 weeks gestational age) who had been followed with sequential developmental assessments for at least 18 months. At the 18 to 24 month evaluation, 31 (18%) had cerebral palsy. We found that using the motor milestones as serial screening tests for cerebral palsy was more effective in terms of positive predictive value than any individual milestone alone. Limited community resources can be more efficiently used if preterm infants with delays in more than four motor milestones are referred for further evaluation and early intervention services.

  9. The discrepancies in multistep damage evolution of yttria-stabilized zirconia irradiated with different ions

    SciTech Connect

    Yang, Tengfei; Taylor, Caitlin A.; Kong, Shuyan; Wang, Chenxu; Zhang, Yanwen; Huang, Xuejun; Xue, Jianming; Yan, Sha; Wang, Yugang

    2013-01-01

    This paper reports a comprehensive investigation of structural damage in yttria-stabilized zirconia irradiated with different ions over a wide fluence range. A similar multistep damage accumulation exists for the irradiations of different ions, but the critical doses for occurrence of second damage step, characterized by a faster increase in damage fraction, and the maximum elastic strain at the first damage step are varied and depend on ion mass. For irradiations of heavier ions, the second damage step occurs at a higher dose with a lower critical elastic strain. Furthermore, larger extended defects were observed in the irradiations of heavy ions at the second damage step. Associated with other experiment results and multistep damage accumulation model, the distinct discrepancies in the damage buildup under irradiations of different ions were interpreted by the effects of electronic excitation, energy of primary knock-on atom and chemistry contributions of deposited ions.

  10. Microtubule dynamic instability: A new model with coupled GTP hydrolysis and multistep catastrophe

    PubMed Central

    Bowne-Anderson, Hugo; Zanic, Marija; Kauer, Monika; Howard, Jonathon

    2013-01-01

    A key question in understanding microtubule dynamics is how GTP hydrolysis leads to catastrophe, the switch from slow growth to rapid shrinkage. We first provide a review of the experimental and modeling literature, and then present a new model of microtubule dynamics. We demonstrate that vectorial, random, and coupled hydrolysis mechanisms are not consistent with the dependence of catastrophe on tubulin concentration and show that, although single-protofilament models can explain many features of dynamics, they do not describe catastrophe as a multistep process. Finally, we present a new combined (coupled plus random hydrolysis) multiple-protofilament model that is a simple, analytically solvable generalization of a single-protofilament model. This model accounts for the observed lifetimes of growing microtubules, the delay to catastrophe following dilution and describes catastrophe as a multistep process. PMID:23532586

  11. Region-based multi-step optic disk and cup segmentation from color fundus image

    NASA Astrophysics Data System (ADS)

    Xiao, Di; Lock, Jane; Manresa, Javier Moreno; Vignarajan, Janardhan; Tay-Kearney, Mei-Ling; Kanagasingam, Yogesan

    2013-02-01

    Retinal optic cup-disk-ratio (CDR) is a one of important indicators of glaucomatous neuropathy. In this paper, we propose a novel multi-step 4-quadrant thresholding method for optic disk segmentation and a multi-step temporal-nasal segmenting method for optic cup segmentation based on blood vessel inpainted HSL lightness images and green images. The performance of the proposed methods was evaluated on a group of color fundus images and compared with the manual outlining results from two experts. Dice scores of detected disk and cup regions between the auto and manual results were computed and compared. Vertical CDRs were also compared among the three results. The preliminary experiment has demonstrated the robustness of the method for automatic optic disk and cup segmentation and its potential value for clinical application.

  12. Intrinsic Micromechanism of Multi-step Structural Transformation in MnNi Shape Memory Alloys

    NASA Astrophysics Data System (ADS)

    Cui, Shushan; Wan, Jianfeng; Rong, Yonghua; Zhang, Jihua

    2017-03-01

    Simulation of the multi-step transformation of cubic matrix → multi-variant tetragonal domain → orthorhombic domain was realized by phase-field method. The intrinsic micromechanism of the second-step transformation in MnNi alloys was studied. It was found that the orthorhombic variant originated from the tetragonal variant with similar orientation, and bar-shaped orthorhombic phase firstly occurred around the interface of twinning bands. The second-step transformation resulted in localized variation of internal stress.

  13. Intrinsic Micromechanism of Multi-step Structural Transformation in MnNi Shape Memory Alloys

    NASA Astrophysics Data System (ADS)

    Cui, Shushan; Wan, Jianfeng; Rong, Yonghua; Zhang, Jihua

    2017-06-01

    Simulation of the multi-step transformation of cubic matrix → multi-variant tetragonal domain → orthorhombic domain was realized by phase-field method. The intrinsic micromechanism of the second-step transformation in MnNi alloys was studied. It was found that the orthorhombic variant originated from the tetragonal variant with similar orientation, and bar-shaped orthorhombic phase firstly occurred around the interface of twinning bands. The second-step transformation resulted in localized variation of internal stress.

  14. Multi-Step Deep Reactive Ion Etching Fabrication Process for Silicon-Based Terahertz Components

    NASA Technical Reports Server (NTRS)

    Jung-Kubiak, Cecile (Inventor); Reck, Theodore (Inventor); Chattopadhyay, Goutam (Inventor); Perez, Jose Vicente Siles (Inventor); Lin, Robert H. (Inventor); Mehdi, Imran (Inventor); Lee, Choonsup (Inventor); Cooper, Ken B. (Inventor); Peralta, Alejandro (Inventor)

    2016-01-01

    A multi-step silicon etching process has been developed to fabricate silicon-based terahertz (THz) waveguide components. This technique provides precise dimensional control across multiple etch depths with batch processing capabilities. Nonlinear and passive components such as mixers and multipliers waveguides, hybrids, OMTs and twists have been fabricated and integrated into a small silicon package. This fabrication technique enables a wafer-stacking architecture to provide ultra-compact multi-pixel receiver front-ends in the THz range.

  15. A multi-step peptidolytic cascade for amino acid recovery in chloroplasts.

    PubMed

    Teixeira, Pedro F; Kmiec, Beata; Branca, Rui M M; Murcha, Monika W; Byzia, Anna; Ivanova, Aneta; Whelan, James; Drag, Marcin; Lehtiö, Janne; Glaser, Elzbieta

    2017-01-01

    Plastids (including chloroplasts) are subcellular sites for a plethora of proteolytic reactions, required in functions ranging from protein biogenesis to quality control. Here we show that peptides generated from pre-protein maturation within chloroplasts of Arabidopsis thaliana are degraded to amino acids by a multi-step peptidolytic cascade consisting of oligopeptidases and aminopeptidases, effectively allowing the recovery of single amino acids within these organelles.

  16. An Undergraduate Organic Chemistry Laboratory Experiment: The Multistep Synthesis of a Modified Nucleoside

    NASA Astrophysics Data System (ADS)

    Delannoy, Peter; Howell, Joseph

    1997-08-01

    We have designed and integrated the multistep synthesis of a modified nucleoside into an undergraduate organic chemistry laboratory. The laboratory was designed as a multidisciplinary approach towards a single synthetic problem. Here we report the synthesis and subsequent purification of 5'-O-dimethoxytrityl-2'-O-methyluridine and 5'-O-dimethoxytrityl-3'-O-methyluridine directly from the literature by a protocol that is appropriate in a small school setting.

  17. Optimal generalized multistep integration formulae for real-time digital simulation

    NASA Technical Reports Server (NTRS)

    Moerder, D. D.; Halyo, N.

    1985-01-01

    The problem of discretizing a dynamical system for real-time digital simulation is considered. Treating the system and its simulation as stochastic processes leads to a statistical characterization of simulator fidelity. A plant discretization procedure based on an efficient matrix generalization of explicit linear multistep discrete integration formulae is introduced, which minimizes a weighted sum of the mean squared steady-state and transient error between the system and simulator outputs.

  18. Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach

    PubMed Central

    Kotera, Masaaki; Tabei, Yasuo; Yamanishi, Yoshihiro; Muto, Ai; Moriya, Yuki; Tokimatsu, Toshiaki; Goto, Susumu

    2014-01-01

    Motivation: Metabolic pathway analysis is crucial not only in metabolic engineering but also in rational drug design. However, the biosynthetic/biodegradation pathways are known only for a small portion of metabolites, and a vast amount of pathways remain uncharacterized. Therefore, an important challenge in metabolomics is the de novo reconstruction of potential reaction networks on a metabolome-scale. Results: In this article, we develop a novel method to predict the multistep reaction sequences for de novo reconstruction of metabolic pathways in the reaction-filling framework. We propose a supervised approach to learn what we refer to as ‘multistep reaction sequence likeness’, i.e. whether a compound–compound pair is possibly converted to each other by a sequence of enzymatic reactions. In the algorithm, we propose a recursive procedure of using step-specific classifiers to predict the intermediate compounds in the multistep reaction sequences, based on chemical substructure fingerprints/descriptors of compounds. We further demonstrate the usefulness of our proposed method on the prediction of enzymatic reaction networks from a metabolome-scale compound set and discuss characteristic features of the extracted chemical substructure transformation patterns in multistep reaction sequences. Our comprehensively predicted reaction networks help to fill the metabolic gap and to infer new reaction sequences in metabolic pathways. Availability and implementation: Materials are available for free at http://web.kuicr.kyoto-u.ac.jp/supp/kot/ismb2014/ Contact: goto@kuicr.kyoto-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24931980

  19. Direct sampling of multiple single-molecular rupture dominant pathways involving a multistep transition.

    PubMed

    Jiang, Huijun; Ding, Huai; Hou, Zhonghuai

    2014-12-14

    We report a novel single-molecular rupture mechanism revealed by direct sampling of the dominant pathway using a self-optimized path sampling method. Multiple dominant pathways involving multistep transitions are identified. The rupture may take place via a direct unfolding from the native state to the unfolding state, or through a two-step pathway bypassing a distinct intermediate metastable state (IMS). This scenario facilitates us to propose a three-state kinetic model, which can produce a nonlinear dependence of the rupture time on pulling forces similar to the ones reported in the literature. In particular, molecule conformations in the IMS maintain an elongation of the tail at one terminal, by which external pulling will enhance the relative stability of IMS. Consequently, even though the overall transition rate of the multistep pathway is relatively small, the molecule still has to be ruptured via the multistep pathway rather than the direct pathway. Thus, our work demonstrates an IMS trapping effect induced rupture mechanism involving an abnormal switching from a fast dominant pathway to a slow one.

  20. Contaminant source and release history identification in groundwater: A multi-step approach

    NASA Astrophysics Data System (ADS)

    Gzyl, G.; Zanini, A.; Frączek, R.; Kura, K.

    2014-02-01

    The paper presents a new multi-step approach aiming at source identification and release history estimation. The new approach consists of three steps: performing integral pumping tests, identifying sources, and recovering the release history by means of a geostatistical approach. The present paper shows the results obtained from the application of the approach within a complex case study in Poland in which several areal sources were identified. The investigated site is situated in the vicinity of a former chemical plant in southern Poland in the city of Jaworzno in the valley of the Wąwolnica River; the plant has been in operation since the First World War producing various chemicals. From an environmental point of view the most relevant activity was the production of pesticides, especially lindane. The application of the multi-step approach enabled a significant increase in the knowledge of contamination at the site. Some suspected contamination sources have been proven to have minor effect on the overall contamination. Other suspected sources have been proven to have key significance. Some areas not taken into consideration previously have now been identified as key sources. The method also enabled estimation of the magnitude of the sources and, a list of the priority reclamation actions will be drawn as a result. The multi-step approach has proven to be effective and may be applied to other complicated contamination cases. Moreover, the paper shows the capability of the geostatistical approach to manage a complex real case study.

  1. Multistep greedy algorithm identifies community structure in real-world and computer-generated networks

    NASA Astrophysics Data System (ADS)

    Schuetz, Philipp; Caflisch, Amedeo

    2008-08-01

    We have recently introduced a multistep extension of the greedy algorithm for modularity optimization. The extension is based on the idea that merging l pairs of communities (l>1) at each iteration prevents premature condensation into few large communities. Here, an empirical formula is presented for the choice of the step width l that generates partitions with (close to) optimal modularity for 17 real-world and 1100 computer-generated networks. Furthermore, an in-depth analysis of the communities of two real-world networks (the metabolic network of the bacterium E. coli and the graph of coappearing words in the titles of papers coauthored by Martin Karplus) provides evidence that the partition obtained by the multistep greedy algorithm is superior to the one generated by the original greedy algorithm not only with respect to modularity, but also according to objective criteria. In other words, the multistep extension of the greedy algorithm reduces the danger of getting trapped in local optima of modularity and generates more reasonable partitions.

  2. Theory of Kinetics of Multistep Ligand-Receptor Assembly in Dissipating and Fluctuating Environments

    NASA Astrophysics Data System (ADS)

    Teslenko, Victor I.; Kapitanchuk, Oleksiy L.

    2013-09-01

    Multistep kinetic processes play a key role in physics (excitation transfer, energy degradation), chemistry (ligand-receptor assembly, radical reactions) and biology (signal perception, molecular recognition). While a phenomenological thermodynamic approach for modeling the elementary acts of transitions underlying the maintaining of a system's stationary and equilibrium states is now well recognized, a more satisfying microscopic description based on the consistent understanding of dissipation and fluctuation processes accompanying the multistep relaxations remains elusive. In this paper, a microscopic theory of kinetics of a few-state system exhibited the energy fluctuations and coupled to a condensed medium is developed. The theory is formulated such as of being an example of the case of irreversible multistep ligand-receptor assembly in a dissipating environment. We first derive general expression for the probability of transitions between the system states valid on the whole timescale and then reduce this expression to the effectively slow times by making it an average over both the steady-state fluctuations of a system's energies and the equilibrium vibrations of the environment. Further, we calculate the populations of states for the sequence of cases of the three-to-two-to-single-step assemblage in dependence on the temperature, viscosity and ligand concentration. Finally, we discuss the results obtained with reference to the case of "negative" cooperativity emerging by virtue of the irreversibility of the last kinetic step.

  3. Multistep-Ahead Air Passengers Traffic Prediction with Hybrid ARIMA-SVMs Models

    PubMed Central

    Ming, Wei; Xiong, Tao

    2014-01-01

    The hybrid ARIMA-SVMs prediction models have been established recently, which take advantage of the unique strength of ARIMA and SVMs models in linear and nonlinear modeling, respectively. Built upon this hybrid ARIMA-SVMs models alike, this study goes further to extend them into the case of multistep-ahead prediction for air passengers traffic with the two most commonly used multistep-ahead prediction strategies, that is, iterated strategy and direct strategy. Additionally, the effectiveness of data preprocessing approaches, such as deseasonalization and detrending, is investigated and proofed along with the two strategies. Real data sets including four selected airlines' monthly series were collected to justify the effectiveness of the proposed approach. Empirical results demonstrate that the direct strategy performs better than iterative one in long term prediction case while iterative one performs better in the case of short term prediction. Furthermore, both deseasonalization and detrending can significantly improve the prediction accuracy for both strategies, indicating the necessity of data preprocessing. As such, this study contributes as a full reference to the planners from air transportation industries on how to tackle multistep-ahead prediction tasks in the implementation of either prediction strategy. PMID:24723814

  4. Evidence for the multistep nature of in vitro human epithelial cell carcinogenesis

    SciTech Connect

    Rhim, J.S.; Yoo, J.H.; Park, J.H.; Thraves, P.; Salehi, Z.; Dritschilo, A. )

    1990-09-01

    In keeping with the multistep development of human cancer in vivo, a stepwise approach to neoplastic transformation in vitro presents a reasonable strategy. We have recently developed an in vitro multistep model suitable for the study of human epithelial cell carcinogenesis. Upon infection with the adenovirus 12-simian virus 40 hybrid virus, primary human epidermal keratinocytes acquired an indefinite life span in culture but did not undergo malignant conversion. Subsequent addition of Kirsten murine sarcoma virus and human ras oncogene or chemical carcinogens (N-methyl-N{prime}-nitro-N-nitrosoguanidine or 4-nitroquinoline 1-oxide) to these cells induced morphological alterations and the acquisition of neoplastic properties. Subsequently it was found that this line could be transformed neoplastically by a variety of retrovirus-containing H-ras, bas, fes, fms, erbB, and src oncogenes. In addition, we found that the immortalized human epidermal keratinocyte (RHEK-1) line can be transformed neoplastically by exposure to ionizing radiation. Thus, this in vitro system may be useful in studying the interaction of a variety of carcinogenic agents and human epithelial cells. These findings demonstrate the malignant transformation of human primary epithelial cells in culture by the combined action of viruses, oncogenes, chemical carcinogens, or X-ray irradiation and support a multistep process for neoplastic conversion.

  5. Photon Production through Multi-step Processes Important in Nuclear Fluorescence Experiments

    SciTech Connect

    Hagmann, C; Pruet, J

    2006-10-26

    The authors present calculations describing the production of photons through multi-step processes occurring when a beam of gamma rays interacts with a macroscopic material. These processes involve the creation of energetic electrons through Compton scattering, photo-absorption and pair production, the subsequent scattering of these electrons, and the creation of energetic photons occurring as these electrons are slowed through Bremsstrahlung emission. Unlike single Compton collisions, during which an energetic photon that is scattered through a large angle loses most of its energy, these multi-step processes result in a sizable flux of energetic photons traveling at large angles relative to an incident photon beam. These multi-step processes are also a key background in experiments that measure nuclear resonance fluorescence by shining photons on a thin foil and observing the spectrum of back-scattered photons. Effective cross sections describing the production of backscattered photons are presented in a tabular form that allows simple estimates of backgrounds expected in a variety of experiments. Incident photons with energies between 0.5 MeV and 8 MeV are considered. These calculations of effective cross sections may be useful for those designing NRF experiments or systems that detect specific isotopes in well-shielded environments through observation of resonance fluorescence.

  6. Protein fabrication automation

    PubMed Central

    Cox, J. Colin; Lape, Janel; Sayed, Mahmood A.; Hellinga, Homme W.

    2007-01-01

    Facile “writing” of DNA fragments that encode entire gene sequences potentially has widespread applications in biological analysis and engineering. Rapid writing of open reading frames (ORFs) for expressed proteins could transform protein engineering and production for protein design, synthetic biology, and structural analysis. Here we present a process, protein fabrication automation (PFA), which facilitates the rapid de novo construction of any desired ORF from oligonucleotides with low effort, high speed, and little human interaction. PFA comprises software for sequence design, data management, and the generation of instruction sets for liquid-handling robotics, a liquid-handling robot, a robust PCR scheme for gene assembly from synthetic oligonucleotides, and a genetic selection system to enrich correctly assembled full-length synthetic ORFs. The process is robust and scalable. PMID:17242375

  7. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools.

    PubMed

    Pineda-Peña, Andrea-Clemencia; Faria, Nuno Rodrigues; Imbrechts, Stijn; Libin, Pieter; Abecasis, Ana Barroso; Deforche, Koen; Gómez-López, Arley; Camacho, Ricardo J; de Oliveira, Tulio; Vandamme, Anne-Mieke

    2013-10-01

    To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3). HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region. The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ~99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic

  8. Identification of feedback loops in neural networks based on multi-step Granger causality.

    PubMed

    Dong, Chao-Yi; Shin, Dongkwan; Joo, Sunghoon; Nam, Yoonkey; Cho, Kwang-Hyun

    2012-08-15

    Feedback circuits are crucial network motifs, ubiquitously found in many intra- and inter-cellular regulatory networks, and also act as basic building blocks for inducing synchronized bursting behaviors in neural network dynamics. Therefore, the system-level identification of feedback circuits using time-series measurements is critical to understand the underlying regulatory mechanism of synchronized bursting behaviors. Multi-Step Granger Causality Method (MSGCM) was developed to identify feedback loops embedded in biological networks using time-series experimental measurements. Based on multivariate time-series analysis, MSGCM used a modified Wald test to infer the existence of multi-step Granger causality between a pair of network nodes. A significant bi-directional multi-step Granger causality between two nodes indicated the existence of a feedback loop. This new identification method resolved the drawback of the previous non-causal impulse response component method which was only applicable to networks containing no co-regulatory forward path. MSGCM also significantly improved the ratio of correct identification of feedback loops. In this study, the MSGCM was testified using synthetic pulsed neural network models and also in vitro cultured rat neural networks using multi-electrode array. As a result, we found a large number of feedback loops in the in vitro cultured neural networks with apparent synchronized oscillation, indicating a close relationship between synchronized oscillatory bursting behavior and underlying feedback loops. The MSGCM is an efficient method to investigate feedback loops embedded in in vitro cultured neural networks. The identified feedback loop motifs are considered as an important design principle responsible for the synchronized bursting behavior in neural networks.

  9. Multistep cascade annihilations of dark matter and the Galactic Center excess

    SciTech Connect

    Elor, Gilly; Rodd, Nicholas L.; Slatyer, Tracy R.

    2015-05-26

    If dark matter is embedded in a non-trivial dark sector, it may annihilate and decay to lighter dark-sector states which subsequently decay to the Standard Model. Such scenarios - with annihilation followed by cascading dark-sector decays - can explain the apparent excess GeV gamma-rays identified in the central Milky Way, while evading bounds from dark matter direct detection experiments. Each 'step' in the cascade will modify the observable signatures of dark matter annihilation and decay, shifting the resulting photons and other final state particles to lower energies and broadening their spectra. We explore, in a model-independent way, the effect of multi-step dark-sector cascades on the preferred regions of parameter space to explain the GeV excess. We find that the broadening effects of multi-step cascades can admit final states dominated by particles that would usually produce too sharply peaked photon spectra; in general, if the cascades are hierarchical (each particle decays to substantially lighter particles), the preferred mass range for the dark matter is in all cases 20-150 GeV. Decay chains that have nearly-degenerate steps, where the products are close to half the mass of the progenitor, can admit much higher DM masses. We map out the region of mass/cross-section parameter space where cascades (degenerate, hierarchical or a combination) can fit the signal, for a range of final states. In the current paper, we study multi-step cascades in the context of explaining the GeV excess, but many aspects of our results are general and can be extended to other applications.

  10. Contaminant source and release history identification in groundwater: a multi-step approach.

    PubMed

    Gzyl, G; Zanini, A; Frączek, R; Kura, K

    2014-02-01

    The paper presents a new multi-step approach aiming at source identification and release history estimation. The new approach consists of three steps: performing integral pumping tests, identifying sources, and recovering the release history by means of a geostatistical approach. The present paper shows the results obtained from the application of the approach within a complex case study in Poland in which several areal sources were identified. The investigated site is situated in the vicinity of a former chemical plant in southern Poland in the city of Jaworzno in the valley of the Wąwolnica River; the plant has been in operation since the First World War producing various chemicals. From an environmental point of view the most relevant activity was the production of pesticides, especially lindane. The application of the multi-step approach enabled a significant increase in the knowledge of contamination at the site. Some suspected contamination sources have been proven to have minor effect on the overall contamination. Other suspected sources have been proven to have key significance. Some areas not taken into consideration previously have now been identified as key sources. The method also enabled estimation of the magnitude of the sources and, a list of the priority reclamation actions will be drawn as a result. The multi-step approach has proven to be effective and may be applied to other complicated contamination cases. Moreover, the paper shows the capability of the geostatistical approach to manage a complex real case study. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Multistep cascade annihilations of dark matter and the Galactic Center excess

    DOE PAGES

    Elor, Gilly; Rodd, Nicholas L.; Slatyer, Tracy R.

    2015-05-26

    If dark matter is embedded in a non-trivial dark sector, it may annihilate and decay to lighter dark-sector states which subsequently decay to the Standard Model. Such scenarios - with annihilation followed by cascading dark-sector decays - can explain the apparent excess GeV gamma-rays identified in the central Milky Way, while evading bounds from dark matter direct detection experiments. Each 'step' in the cascade will modify the observable signatures of dark matter annihilation and decay, shifting the resulting photons and other final state particles to lower energies and broadening their spectra. We explore, in a model-independent way, the effect ofmore » multi-step dark-sector cascades on the preferred regions of parameter space to explain the GeV excess. We find that the broadening effects of multi-step cascades can admit final states dominated by particles that would usually produce too sharply peaked photon spectra; in general, if the cascades are hierarchical (each particle decays to substantially lighter particles), the preferred mass range for the dark matter is in all cases 20-150 GeV. Decay chains that have nearly-degenerate steps, where the products are close to half the mass of the progenitor, can admit much higher DM masses. We map out the region of mass/cross-section parameter space where cascades (degenerate, hierarchical or a combination) can fit the signal, for a range of final states. In the current paper, we study multi-step cascades in the context of explaining the GeV excess, but many aspects of our results are general and can be extended to other applications.« less

  12. Expression Patterns of Cancer Stem Cell Markers During Specific Celecoxib Therapy in Multistep Rat Colon Carcinogenesis Bioassays.

    PubMed

    Salim, Elsayed I; Hegazi, Mona M; Kang, Jin Seok; Helmy, Hager M

    2016-01-01

    The purpose of this study was to investigate the role of colon cancer stem cells (CSCs) during chemicallyinduced rat multi-step colon carcinogenesis with or without the treatment with a specific cyclooxygenase-2 inhibitor drug (celecoxib). Two experiments were performed, the first, a short term 12 week colon carcinogenesis bioassay in which only surrogate markers for colon cancer, aberrant crypt foci (ACF) lesions, were formed. The other experiment was a medium term colon cancer rat assay in which tumors had developed after 32 weeks. Treatment with celecoxib lowered the numbers of ACF, as well as the tumor volumes and multiplicities after 32 weeks. Immunohistochemical proliferating cell nuclear antigen (PCNA) labeling indexes LI (%) were downregulated after treatment by celecoxib. Also different cell surface antigens known to associate with CSCs such as the epithelial cell adhesion molecule (EpCAM), CD44 and CD133 were compared between the two experiments and showed differential expression patterns depending on the stage of carcinogenesis and treatment with celecoxib. Flow cytometric analysis demonstrated that the numbers of CD133 cells were increased in the colonic epithelium after 12 weeks while those of CD44 but not CD133 cells were increased after 32 weeks. Moreover, aldehyde dehydrogenase-1 activity levels in the colonic epithelium (a known CSC marker) detected by ELISA assay were found down-regulated after 12 weeks, but were up-regulated after 32 weeks. The data have also shown that the protective effect of celecoxib on these specific markers and populations of CSCs and on other molecular processes such as apoptosis targeted by this drug may vary depending on the genetic and phenotypic stages of carcinogenesis. Therefore, uncovering these distinction roles of CSCs during different phases of carcinogenesis and during specific treatment could be useful for targeted therapy.

  13. Epigenetic Genes and Emotional Reactivity to Daily Life Events: A Multi-Step Gene-Environment Interaction Study

    PubMed Central

    Pishva, Ehsan; Drukker, Marjan; Viechtbauer, Wolfgang; Decoster, Jeroen; Collip, Dina; van Winkel, Ruud; Wichers, Marieke; Jacobs, Nele; Thiery, Evert; Derom, Catherine; Geschwind, Nicole; van den Hove, Daniel; Lataster, Tineke; Myin-Germeys, Inez; van Os, Jim

    2014-01-01

    Recent human and animal studies suggest that epigenetic mechanisms mediate the impact of environment on development of mental disorders. Therefore, we hypothesized that polymorphisms in epigenetic-regulatory genes impact stress-induced emotional changes. A multi-step, multi-sample gene-environment interaction analysis was conducted to test whether 31 single nucleotide polymorphisms (SNPs) in epigenetic-regulatory genes, i.e. three DNA methyltransferase genes DNMT1, DNMT3A, DNMT3B, and methylenetetrahydrofolate reductase (MTHFR), moderate emotional responses to stressful and pleasant stimuli in daily life as measured by Experience Sampling Methodology (ESM). In the first step, main and interactive effects were tested in a sample of 112 healthy individuals. Significant associations in this discovery sample were then investigated in a population-based sample of 434 individuals for replication. SNPs showing significant effects in both the discovery and replication samples were subsequently tested in three other samples of: (i) 85 unaffected siblings of patients with psychosis, (ii) 110 patients with psychotic disorders, and iii) 126 patients with a history of major depressive disorder. Multilevel linear regression analyses showed no significant association between SNPs and negative affect or positive affect. No SNPs moderated the effect of pleasant stimuli on positive affect. Three SNPs of DNMT3A (rs11683424, rs1465764, rs1465825) and 1 SNP of MTHFR (rs1801131) moderated the effect of stressful events on negative affect. Only rs11683424 of DNMT3A showed consistent directions of effect in the majority of the 5 samples. These data provide the first evidence that emotional responses to daily life stressors may be moderated by genetic variation in the genes involved in the epigenetic machinery. PMID:24967710

  14. Epigenetic genes and emotional reactivity to daily life events: a multi-step gene-environment interaction study.

    PubMed

    Pishva, Ehsan; Drukker, Marjan; Viechtbauer, Wolfgang; Decoster, Jeroen; Collip, Dina; van Winkel, Ruud; Wichers, Marieke; Jacobs, Nele; Thiery, Evert; Derom, Catherine; Geschwind, Nicole; van den Hove, Daniel; Lataster, Tineke; Myin-Germeys, Inez; van Os, Jim; Rutten, Bart P F; Kenis, Gunter

    2014-01-01

    Recent human and animal studies suggest that epigenetic mechanisms mediate the impact of environment on development of mental disorders. Therefore, we hypothesized that polymorphisms in epigenetic-regulatory genes impact stress-induced emotional changes. A multi-step, multi-sample gene-environment interaction analysis was conducted to test whether 31 single nucleotide polymorphisms (SNPs) in epigenetic-regulatory genes, i.e. three DNA methyltransferase genes DNMT1, DNMT3A, DNMT3B, and methylenetetrahydrofolate reductase (MTHFR), moderate emotional responses to stressful and pleasant stimuli in daily life as measured by Experience Sampling Methodology (ESM). In the first step, main and interactive effects were tested in a sample of 112 healthy individuals. Significant associations in this discovery sample were then investigated in a population-based sample of 434 individuals for replication. SNPs showing significant effects in both the discovery and replication samples were subsequently tested in three other samples of: (i) 85 unaffected siblings of patients with psychosis, (ii) 110 patients with psychotic disorders, and iii) 126 patients with a history of major depressive disorder. Multilevel linear regression analyses showed no significant association between SNPs and negative affect or positive affect. No SNPs moderated the effect of pleasant stimuli on positive affect. Three SNPs of DNMT3A (rs11683424, rs1465764, rs1465825) and 1 SNP of MTHFR (rs1801131) moderated the effect of stressful events on negative affect. Only rs11683424 of DNMT3A showed consistent directions of effect in the majority of the 5 samples. These data provide the first evidence that emotional responses to daily life stressors may be moderated by genetic variation in the genes involved in the epigenetic machinery.

  15. Automated Assay of Telomere Length Measurement and Informatics for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort.

    PubMed

    Lapham, Kyle; Kvale, Mark N; Lin, Jue; Connell, Sheryl; Croen, Lisa A; Dispensa, Brad P; Fang, Lynn; Hesselson, Stephanie; Hoffmann, Thomas J; Iribarren, Carlos; Jorgenson, Eric; Kushi, Lawrence H; Ludwig, Dana; Matsuguchi, Tetsuya; McGuire, William B; Miles, Sunita; Quesenberry, Charles P; Rowell, Sarah; Sadler, Marianne; Sakoda, Lori C; Smethurst, David; Somkin, Carol P; Van Den Eeden, Stephen K; Walter, Lawrence; Whitmer, Rachel A; Kwok, Pui-Yan; Risch, Neil; Schaefer, Catherine; Blackburn, Elizabeth H

    2015-08-01

    The Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH) Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort includes DNA specimens extracted from saliva samples of 110,266 individuals. Because of its relationship to aging, telomere length measurement was considered an important biomarker to develop on these subjects. To assay relative telomere length (TL) on this large cohort over a short time period, we created a novel high throughput robotic system for TL analysis and informatics. Samples were run in triplicate, along with control samples, in a randomized design. As part of quality control, we determined the within-sample variability and employed thresholds for the elimination of outlying measurements. Of 106,902 samples assayed, 105,539 (98.7%) passed all quality control (QC) measures. As expected, TL in general showed a decline with age and a sex difference. While telomeres showed a negative correlation with age up to 75 years, in those older than 75 years, age positively correlated with longer telomeres, indicative of an association of longer telomeres with more years of survival in those older than 75. Furthermore, while females in general had longer telomeres than males, this difference was significant only for those older than age 50. An additional novel finding was that the variance of TL between individuals increased with age. This study establishes reliable assay and analysis methodologies for measurement of TL in large, population-based human studies. The GERA cohort represents the largest currently available such resource, linked to comprehensive electronic health and genotype data for analysis.

  16. Automated Assay of Telomere Length Measurement and Informatics for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

    PubMed Central

    Lapham, Kyle; Kvale, Mark N.; Lin, Jue; Connell, Sheryl; Croen, Lisa A.; Dispensa, Brad P.; Fang, Lynn; Hesselson, Stephanie; Hoffmann, Thomas J.; Iribarren, Carlos; Jorgenson, Eric; Kushi, Lawrence H.; Ludwig, Dana; Matsuguchi, Tetsuya; McGuire, William B.; Miles, Sunita; Quesenberry, Charles P.; Rowell, Sarah; Sadler, Marianne; Sakoda, Lori C.; Smethurst, David; Somkin, Carol P.; Van Den Eeden, Stephen K.; Walter, Lawrence; Whitmer, Rachel A.; Kwok, Pui-Yan; Risch, Neil; Schaefer, Catherine; Blackburn, Elizabeth H.

    2015-01-01

    The Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH) Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort includes DNA specimens extracted from saliva samples of 110,266 individuals. Because of its relationship to aging, telomere length measurement was considered an important biomarker to develop on these subjects. To assay relative telomere length (TL) on this large cohort over a short time period, we created a novel high throughput robotic system for TL analysis and informatics. Samples were run in triplicate, along with control samples, in a randomized design. As part of quality control, we determined the within-sample variability and employed thresholds for the elimination of outlying measurements. Of 106,902 samples assayed, 105,539 (98.7%) passed all quality control (QC) measures. As expected, TL in general showed a decline with age and a sex difference. While telomeres showed a negative correlation with age up to 75 years, in those older than 75 years, age positively correlated with longer telomeres, indicative of an association of longer telomeres with more years of survival in those older than 75. Furthermore, while females in general had longer telomeres than males, this difference was significant only for those older than age 50. An additional novel finding was that the variance of TL between individuals increased with age. This study establishes reliable assay and analysis methodologies for measurement of TL in large, population-based human studies. The GERA cohort represents the largest currently available such resource, linked to comprehensive electronic health and genotype data for analysis. PMID:26092717

  17. PRE-ADAMO: a multi-step approach for the identification of life on Mars

    NASA Astrophysics Data System (ADS)

    Brucato, J. R.; Vázquez, L.; Rotundi, A.; Cataldo, F.; Palomba, E.; Saladino, R.; di Mauro, E.; Baratta, G.; Barbier, B.; Battaglia, R.; Colangeli, L.; Costanzo, G.; Crestini, C.; della Corte, V.; Mazzotta Epifani, E.; Esposito, F.; Ferrini, G.; Gómez Elvira, J.; Isola, M.; Keheyan, Y.; Leto, G.; Martinez Frias, J.; Mennella, V.; Negri, R.; Palumbo, M. E.; Palumbo, P.; Strazzulla, G.; Falciani, P.; Adami, G.; Guizzo, G. P.; Campiotti, S.

    2004-03-01

    It is of paramount importance to detect traces of life on Mars surface. Organic molecules are highly polar and if present on Mars require to be extracted from the dust sample, separated, concentrated, processed and analysed by an appropriate apparatus. PRE-ADAMO (PRebiotic Experiment - Activity of Dust And bioMolecules Observation) is a multi-steps approach for the identification of possible polar substances present on Mars. It was proposed as instrument of Pasteur payload for the ESA (European Space Agency) ExoMars rover mission. Main scientific objectives and experimental approach of PRE-ADAMO are here presented.

  18. Multistepped Drill Design for Single-Stage Implant Site Preparation: Experimental Study in Type 2 Bone.

    PubMed

    Abboud, Marcus; Delgado-Ruiz, Rafael Arcesio; Kucine, Allan; Rugova, Sihana; Balanta, Julian; Calvo-Guirado, Jose Luis

    2015-10-01

    To evaluate an experimental multistepped drill for single-stage implant site preparation by means of real-time analysis of thermal variations during and postdrilling, and by implant stability evaluation. Temperature and time were recorded in real time by paired microprobe thermocouples during simulated osteotomy in type 2 bone similes at the cortical and cancellous zones. Three different drilling groups with a new multistepped drill design were compared: Control (2-mm diameter pilot drill + 3.3-mm three-stepped drill + 4.1-mm three-stepped drill); Test A (3.3-mm three-stepped drill); and Test B (4.1-mm three-stepped drill). Implants were inserted, and implant stability was evaluated with the Perio Test Value (PTV). Two-way anova was used to test the independent effects of osteotomy and implant diameter on temperature and stability. All the drills induced thermal changes without significant differences between groups (p > .05). Drilling in cortical bone produced significant increase of the temperatures in a range of 1.8 ± 0.9°C compared with drilling in cancellous bone (p < .05). ΔT temperatures were significantly higher for test groups in cortical and cancellous bone (p < .05); ΔT10 for all groups showed a reduction of the temperature in a range of 1.7 ± 0.3°C without significant differences between groups (p > .05); the mean time to accomplish drilling was significantly longer in the control group (p < .05); test groups took 10 ± 0.3 seconds less to reach the required drilling depth. PTV values were higher in test groups compared with controls (p < .05). The multistepped drills used for single-stage implant site preparation Increase temperature as in comparison with a conventional incremental protocol; Induce the temperature increment in cortical bone compared with the cancellous bone; Reduce drilling time when a multistepped drill is used alone; and Increase implant stability twofold compared with a conventional

  19. Multistep liquid-phase lithography for fast prototyping of microfluidic free-flow-electrophoresis chips.

    PubMed

    Jezierski, Stefan; Gitlin, Leonid; Nagl, Stefan; Belder, Detlev

    2011-11-01

    We present a fast and versatile method to produce functional micro free-flow electrophoresis chips. Microfluidic structures were generated between two glass slides applying multistep liquid-phase lithography, omitting troublesome bonding steps or cost-intensive master structures. Utilizing a novel spacer-less approach with the photodefinable polymer polyethyleneglycol dimethacrylate (PEG-DA), microfluidic devices with hydrophilic channels of only 25 μm in height were generated. The microfluidic chips feature ion-permeable segregation walls between the electrode channels and the separation bed and hydrophilic surfaces. The performance of the chip is demonstrated by free-flow electrophoretic separation of fluorescent xanthene dyes and fluorescently labeled amino acids.

  20. Model of multistep electron transfer in a single-mode polar medium

    NASA Astrophysics Data System (ADS)

    Feskov, S. V.; Yudanov, V. V.

    2017-09-01

    A mathematical model of multistep photoinduced electron transfer (PET) in a polar medium with a single relaxation time (Debye solvent) is developed. The model includes the polarization nonequilibrity formed in the vicinity of the donor-acceptor molecular system at the initial steps of photoreaction and its influence on the subsequent steps of PET. It is established that the results from numerical simulation of transient luminescence spectra of photoexcited donor-acceptor complexes (DAC) conform to calculated data obtained on the basis of the familiar experimental technique used to measure the relaxation function of solvent polarization in the vicinity of DAC in the picosecond and subpicosecond ranges.

  1. Analysis of intrinsic coupling loss in multi-step index optical fibres.

    PubMed

    Aldabaldetreku, Gotzon; Durana, Gaizka; Zubia, Joseba; Arrue, Jon; Jiménez, Felipe; Mateo, Javier

    2005-05-02

    The main goal of the present paper is to provide a comprehensive analysis of the intrinsic coupling loss for multi-step index (MSI) fibres and compare it with those obtained for step- and graded-index fibres. We investigate the effects of tolerances to each waveguide parameter typical in standard manufacturing processes by carrying out several simulations using the ray-tracing method. The results obtained will serve us to identify the most critical waveguide variations to which fibre manufactures will have to pay closer attention to achieve lower coupling losses.

  2. The microbial cell-functional unit for energy dependent multistep biocatalysis.

    PubMed

    Ladkau, Nadine; Schmid, Andreas; Bühler, Bruno

    2014-12-01

    Whole-cell biocatalysis has emerged as an important tool for the synthesis of value-added fine and bulk chemicals as well as pharmaceuticals. Especially, the rapid development of recombinant DNA technologies resulted in a shift from the exploitation of natural enzymes and pathways to the design of recombinant cell factories comprising heterologous enzymes and/or synthetic, orthologous pathways for the synthesis of industrially relevant compounds. This review discusses recent developments and concepts applied in the frame of multistep whole-cell biocatalysis along with representative examples. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Synergy between chemo- and bio-catalysts in multi-step transformations.

    PubMed

    Caiazzo, Aldo; Garcia, Paula M L; Wever, Ron; van Hest, Jan C M; Rowan, Alan E; Reek, Joost N H

    2009-07-21

    Cascade synthetic pathways, which allow multi-step conversions to take place in one reaction vessel, are crucial for the development of biomimetic, highly efficient new methods of chemical synthesis. Theoretically, the complexity introduced by combining processes could lead to an improvement of the overall process; however, it is the current general belief that it is more efficient to run processes separately. Inspired by natural cascade procedures we successfully combined a lipase catalyzed amidation with palladium catalyzed coupling reactions, simultaneously carried out on the same molecule. Unexpectedly, the bio- and chemo-catalyzed processes show synergistic behaviour, highlighting the complexity of multi-catalyst systems.

  4. Autonomy and Automation

    NASA Technical Reports Server (NTRS)

    Shively, Jay

    2017-01-01

    A significant level of debate and confusion has surrounded the meaning of the terms autonomy and automation. Automation is a multi-dimensional concept, and we propose that Remotely Piloted Aircraft Systems (RPAS) automation should be described with reference to the specific system and task that has been automated, the context in which the automation functions, and other relevant dimensions. In this paper, we present definitions of automation, pilot in the loop, pilot on the loop and pilot out of the loop. We further propose that in future, the International Civil Aviation Organization (ICAO) RPAS Panel avoids the use of the terms autonomy and autonomous when referring to automated systems on board RPA. Work Group 7 proposes to develop, in consultation with other workgroups, a taxonomy of Levels of Automation for RPAS.

  5. Automated tetraploid genotype calling by hierarchical clustering

    USDA-ARS?s Scientific Manuscript database

    SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, however, the relationship between signal intensity and allele dosage must be inferred independently for each marker. We developed an improved computational method to automate this process, ...

  6. Workflow automation architecture standard

    SciTech Connect

    Moshofsky, R.P.; Rohen, W.T.

    1994-11-14

    This document presents an architectural standard for application of workflow automation technology. The standard includes a functional architecture, process for developing an automated workflow system for a work group, functional and collateral specifications for workflow automation, and results of a proof of concept prototype.

  7. A multistep screening method to identify genes using evolutionary transcriptome of plants.

    PubMed

    Kim, Chang-Kug; Lim, Hye-Min; Na, Jong-Kuk; Choi, Ji-Weon; Sohn, Seong-Han; Park, Soo-Chul; Kim, Young-Hwan; Kim, Yong-Kab; Kim, Dool-Yi

    2014-01-01

    We introduced a multistep screening method to identify the genes in plants using microarrays and ribonucleic acid (RNA)-seq transcriptome data. Our method describes the process for identifying genes using the salt-tolerance response pathways of the potato (Solanum tuberosum) plant. Gene expression was analyzed using microarrays and RNA-seq experiments that examined three potato lines (high, intermediate, and low salt tolerance) under conditions of salt stress. We screened the orthologous genes and pathway genes involved in salinity-related biosynthetic pathways, and identified nine potato genes that were candidates for salinity-tolerance pathways. The nine genes were selected to characterize their phylogenetic reconstruction with homologous genes of Arabidopsis thaliana, and a Circos diagram was generated to understand the relationships among the selected genes. The involvement of the selected genes in salt-tolerance pathways was verified by reverse transcription polymerase chain reaction analysis. One candidate potato gene was selected for physiological validation by generating dehydration-responsive element-binding 1 (DREB1)-overexpressing transgenic potato plants. The DREB1 overexpression lines exhibited increased salt tolerance and plant growth when compared to that of the control. Although the nine genes identified by our multistep screening method require further characterization and validation, this study demonstrates the power of our screening strategy after the initial identification of genes using microarrays and RNA-seq experiments.

  8. A multi-step method for material decomposition in spectral computed tomography

    NASA Astrophysics Data System (ADS)

    Fredette, Nathaniel R.; Lewis, Cale E.; Das, Mini

    2017-03-01

    When using a photon counting detector for material decomposition problems, a major issue is the low-count rate per energy bin which may lead to high image-noise with compromised contrast and accuracy. A multi-step algorithmic method of material decomposition is proposed for spectral computed tomography (CT), where the problem is formulated as series of simpler and dose efficient decompositions rather than solved simultaneously. A simple domain of four materials; water, hydroxyapatite, iodine and gold was explored. The results showed an improvement in accuracy with low-noise over a similar method where the materials were decomposed simultaneously. In the multi-step approach, for the same acquired energy bin data, the problem is reformulated in each step with decreasing number of energy bins (resulting in a higher count levels per bin) and unknowns in each step. This offers flexibility in the choice of energy bins for each material type. Our results are very preliminary but show promise and potential to tackle challenging decomposition tasks. Complete work will include detailed analysis of this approach and experimental data with more complex mixtures.

  9. Formation of Stone-Wales edge: Multistep reconstruction and growth mechanisms of zigzag nanographene.

    PubMed

    Dang, Jing-Shuang; Wang, Wei-Wei; Zheng, Jia-Jia; Nagase, Shigeru; Zhao, Xiang

    2017-10-05

    Although the existence of Stone-Wales (5-7) defect at graphene edge has been clarified experimentally, theoretical study on the formation mechanism is still imperfect. In particular, the regioselectivity of multistep reactions at edge (self-reconstruction and growth with foreign carbon feedstock) is essential to understand the kinetic behavior of reactive boundaries but investigations are still lacking. Herein, by using finite-sized models, multistep reconstructions and carbon dimer additions of a bared zigzag edge are introduced using density functional theory calculations. The zigzag to 5-7 transformation is proved as a site-selective process to generate alternating 5-7 pairs sequentially and the first step with largest barrier is suggested as the rate-determining step. Conversely, successive C2 insertions on the active edge are calculated to elucidate the formation of 5-7 edge during graphene growth. A metastable intermediate with a triple sequentially fused pentagon fragment is proved as the key structure for 5-7 edge formation. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  10. Research on processing medicinal herbs with multi-steps infrared macro-fingerprint method.

    PubMed

    Yu, Lu; Sun, Su-Qin; Fan, Ke-Feng; Zhou, Qun; Noda, Isao

    2005-11-01

    How to apply rapid and effective method to research medicinal herbs, the representative of complicated mixture system, is the current study focus for analysts. The functions of non-processed and processed medicinal herbs are greatly different, so controlling the processing procedure is highly important for guarantee of the curative effect. Almost, the conventional criteria of processing are based on personal sensory experience. There is no scientific and impersonal benchmark. In this article, we take Rehmannia for example, conducting a systematic study on the process of braising Rehmannia with yellow wine by using the multi-steps infrared (IR) macro-fingerprint method. The method combines three steps: conventional Fourier transform infrared spectroscopy (FT-IR), second derivative spectroscopy, and two-dimensional infrared (2D-IR) correlation spectroscopy. Based on the changes in different types of IR spectra during the process, we can infer the optimal end-point of processing Rehmannia and the main transformations during the process. The result provides a scientific explanation to the traditional sensory experience based recipe: the end-point product is "dark as night and sweet as malt sugar". In conclusion, the multi-steps IR macro-fingerprint method, which is rapid and reasonable, can play an important role in controlling the processing of medicinal herbs.

  11. A new multistep Ca2+-induced cold gelation process for beta-lactoglobulin.

    PubMed

    Veerman, Cecile; Baptist, Harry; Sagis, Leonard M C; van der Linden, Erik

    2003-06-18

    The objective of this study was to obtain beta-lactoglobulin (beta-lg) gels at very low protein concentrations using a new multistep Ca(2+)-induced cold gelation process. In the conventional cold gelation process, salt free beta-lg solutions were heated at neutral pH, cooled, and cross-linked by adding salts. In our new process, first, long linear beta-lg fibrils were formed at pH 2. Solutions of these fibrils were cooled, and subsequently, the pH was adjusted to 7 or 8. Transmission electron microscopy studies showed that the long linear fibrils formed at pH 2 were stable when the pH was adjusted to 7 or 8. In the final step, the fibrils were cross-linked using CaCl(2). Using rheological measurements, the critical percolation concentration was determined. In the new multistep cold gelation process, the critical percolation concentration was an order of magnitude lower than in the conventional cold gelation method.

  12. A multi-step assembly process: drawing, flanging and hemming of metallic sheets

    NASA Astrophysics Data System (ADS)

    Manach, P. Y.; Le Maoût, N.; Thuillier, S.

    2010-06-01

    This paper presents hemming tests on complex geometries, combining curved surfaces and radii of curvature in the plane. The samples are firstly prestrained in order to obtain a strain history prior to flanging and hemming. The choice of the sample geometries as well as prior plastic strains is based on a survey of current geometries hemmed in automotive doors. A device has been designed to hem these samples both by classical and roll-hemming processes and to allow a comparison between both technologies. Roll-in, which characterizes the change of geometry of the hemmed zone between flanging and hemming, and loads are obtained during this multistep process. Results show that roll-in observed in roll-hemming is lower than in classical hemming and that its evolution greatly differs between the two processes. The analysis of the results on different samples shows that it is difficult to establish rules on the variation of other parameters in such a complex multistep process and that it requires an intensive use of numerical simulation.

  13. PSO-MISMO modeling strategy for multistep-ahead time series prediction.

    PubMed

    Bao, Yukun; Xiong, Tao; Hu, Zhongyi

    2014-05-01

    Multistep-ahead time series prediction is one of the most challenging research topics in the field of time series modeling and prediction, and is continually under research. Recently, the multiple-input several multiple-outputs (MISMO) modeling strategy has been proposed as a promising alternative for multistep-ahead time series prediction, exhibiting advantages compared with the two currently dominating strategies, the iterated and the direct strategies. Built on the established MISMO strategy, this paper proposes a particle swarm optimization (PSO)-based MISMO modeling strategy, which is capable of determining the number of sub-models in a self-adaptive mode, with varying prediction horizons. Rather than deriving crisp divides with equal-size s prediction horizons from the established MISMO, the proposed PSO-MISMO strategy, implemented with neural networks, employs a heuristic to create flexible divides with varying sizes of prediction horizons and to generate corresponding sub-models, providing considerable flexibility in model construction, which has been validated with simulated and real datasets.

  14. Chiral transformation in protonated and deprotonated adipic acids through multistep internal proton transfer.

    PubMed

    Min, Seung Kyu; Park, Mina; Singh, N Jiten; Lee, Han Myoung; Lee, Eun Cheol; Kim, Kwang S; Lagutschenkov, Anita; Niedner-Schatteburg, Gereon

    2010-09-10

    Protonated and deprotonated adipic acids (PAA: HOOC-(CH(2))(4)--COOH(2) (+) and DAA: HOOC-(CH(2))(4)-COO(-)) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H(2)O...H...OH(2))(+) Zundel-like symmetric hydrogen bonding, whereas that of DAA has H(3)O(+) Eigen-like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel-like ions for PAA and Eigen-like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH...O short hydrogen-bond stretching peaks are predicted in the range of 1000-1700 cm(-1) in the Car-Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen-bond peaks. The O-H-O stretching peaks in the range of 1800-2700 cm(-1) become insignificant above around 150 K and are almost washed out at about 300 K.

  15. Multistep Model of Cervical Cancer: Participation of miRNAs and Coding Genes

    PubMed Central

    López, Angelica Judith Granados; López, Jesús Adrián

    2014-01-01

    Aberrant miRNA expression is well recognized as an important step in the development of cancer. Close to 70 microRNAs (miRNAs) have been implicated in cervical cancer up to now, nevertheless it is unknown if aberrant miRNA expression causes the onset of cervical cancer. One of the best ways to address this issue is through a multistep model of carcinogenesis. In the progression of cervical cancer there are three well-established steps to reach cancer that we used in the model proposed here. The first step of the model comprises the gene changes that occur in normal cells to be transformed into immortal cells (CIN 1), the second comprises immortal cell changes to tumorigenic cells (CIN 2), the third step includes cell changes to increase tumorigenic capacity (CIN 3), and the final step covers tumorigenic changes to carcinogenic cells. Altered miRNAs and their target genes are located in each one of the four steps of the multistep model of carcinogenesis. miRNA expression has shown discrepancies in different works; therefore, in this model we include miRNAs recording similar results in at least two studies. The present model is a useful insight into studying potential prognostic, diagnostic, and therapeutic miRNAs. PMID:25192291

  16. Multistep model of cervical cancer: participation of miRNAs and coding genes.

    PubMed

    Granados López, Angelica Judith; López, Jesús Adrián

    2014-09-04

    Aberrant miRNA expression is well recognized as an important step in the development of cancer. Close to 70 microRNAs (miRNAs) have been implicated in cervical cancer up to now, nevertheless it is unknown if aberrant miRNA expression causes the onset of cervical cancer. One of the best ways to address this issue is through a multistep model of carcinogenesis. In the progression of cervical cancer there are three well-established steps to reach cancer that we used in the model proposed here. The first step of the model comprises the gene changes that occur in normal cells to be transformed into immortal cells (CIN 1), the second comprises immortal cell changes to tumorigenic cells (CIN 2), the third step includes cell changes to increase tumorigenic capacity (CIN 3), and the final step covers tumorigenic changes to carcinogenic cells. Altered miRNAs and their target genes are located in each one of the four steps of the multistep model of carcinogenesis. miRNA expression has shown discrepancies in different works; therefore, in this model we include miRNAs recording similar results in at least two studies. The present model is a useful insight into studying potential prognostic, diagnostic, and therapeutic miRNAs.

  17. Electrochemical Biosensor: Multistep functionalization of thiolated ssDNA on gold-coated microcantilever

    NASA Astrophysics Data System (ADS)

    Dulanto Carbajal, Jorge

    Bio-chemical sensors are an emerging and vibrant area of research. The use of micromechanical cantilevers is relatively new as biomechanical recognition detectors. Reactions on a gold coated and chemically functionalized surface produce a mechanical deflection of the cantilever which is used as the input signal of the detector. Within the area of biosensors, DNA-sensors have a wide range of applications such as DNA hybridization detectors, DNA mismatch sequence detectors and protein detectors. We designed and built a microcantilever sensor system which allows for control and characterization of surface conditions. This includes controlled functionalization which can be a dominant factor in signal generation and reproducibility in these systems. Additionally, we developed a multistep functionalization protocol which consists of a sequence of short incubations and characterizations of thiolated ssDNA on a gold-coated cantilever. Multistep functionalization is a new protocol that is used to control the ssDNA surface density on a gold-coated cantilever. Repeatable responses and feasible biosensors are obtained using this protocol.

  18. Adaptive multi-step Full Waveform Inversion based on Waveform Mode Decomposition

    NASA Astrophysics Data System (ADS)

    Hu, Yong; Han, Liguo; Xu, Zhuo; Zhang, Fengjiao; Zeng, Jingwen

    2017-04-01

    Full Waveform Inversion (FWI) can be used to build high resolution velocity models, but there are still many challenges in seismic field data processing. The most difficult problem is about how to recover long-wavelength components of subsurface velocity models when seismic data is lacking of low frequency information and without long-offsets. To solve this problem, we propose to use Waveform Mode Decomposition (WMD) method to reconstruct low frequency information for FWI to obtain a smooth model, so that the initial model dependence of FWI can be reduced. In this paper, we use adjoint-state method to calculate the gradient for Waveform Mode Decomposition Full Waveform Inversion (WMDFWI). Through the illustrative numerical examples, we proved that the low frequency which is reconstructed by WMD method is very reliable. WMDFWI in combination with the adaptive multi-step inversion strategy can obtain more faithful and accurate final inversion results. Numerical examples show that even if the initial velocity model is far from the true model and lacking of low frequency information, we still can obtain good inversion results with WMD method. From numerical examples of anti-noise test, we see that the adaptive multi-step inversion strategy for WMDFWI has strong ability to resist Gaussian noise. WMD method is promising to be able to implement for the land seismic FWI, because it can reconstruct the low frequency information, lower the dominant frequency in the adjoint source, and has a strong ability to resist noise.

  19. A multi-step kinetic model for substrate assimilation and bacterial growth: application to benzene biodegradation.

    PubMed

    Bordel, S; Muñoz, R; Díaz, L F; Villaverde, S

    2007-08-01

    A multi-step kinetic model based on the concept of synthesizing unit (SU) was developed for describing benzene biodegradation in Pseudomonas putida F1. The model herein presented considered substrate arrival rates to the SU rather than concentrations, and provided a reasonable good fit of the dynamics of both catechol and biomass concentrations experimentally determined. It was based on very general assumptions and could be applied to any process accumulating metabolic intermediates. Conventional growth models considering a single step can be regarded as a particular case of this multi-step model. Despite the merits of this model, its applicability strongly depends on the knowledge of the complex induction-repression and inhibition mechanisms governing the different catabolic steps of the degradation pathway, which in most cases are difficult to elucidate experimentally and/or to model mathematically. In this particular case repression of benzene oxidation by catechol and self-inhibition of catechol transformation were experimentally confirmed and considered in the simulation, resulting in a good fit (relative average error of 6%) of the experimental data. (c) 2007 Wiley Periodicals, Inc.

  20. Forming Analysis of AZ31 Magnesium Alloy Sheets by Means of a Multistep Inverse Approach

    SciTech Connect

    Nguyen, Ba Nghiep; Bapanapalli, Satish K.

    2009-04-01

    This paper applies a multi-step inverse approach to predict the forming of AZ31 magnesium alloy sheets. An in-house finite element code named “INAPH”, which implements the inverse approach formulation by Guo et al. (Int. J. Numer. Methods Eng., 30, 1385-1401), has been used for the forming analysis. This inverse approach uses the deformation theory of plasticity and assumes that the deformation is independent of the loading history. Failure during forming is predicted by a stress-based criterion or a forming limit diagram-based criterion. The INAPH predictions have been compared with experimental results of Takuda et al (Journal of Materials Processing Technology, 89-90:135-140) and incremental analysis using ABAQUS. The multi-step inverse analysis has been shown to very quickly and fairly accurately predict stress, plastic strain, thickness distributions and failure locations on deeply drawn parts made of AZ31 magnesium alloy. The capability of INAPH to predict the formability of magnesium alloys has also been demonstrated at various temperatures. As magnesium alloys possess very limited formability at room temperature, and their formability becomes better at higher temperatures (> 100oC), the inverse analysis constitutes an efficient and valuable tool to predict forming of magnesium alloy parts as a function of temperature. In addition, other processing and design parameters such as the initial dimensions, final desired shape, blank holder forces, and friction can be quickly adjusted to assess the forming feasibility.

  1. Automation in Clinical Microbiology

    PubMed Central

    Ledeboer, Nathan A.

    2013-01-01

    Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories. PMID:23515547

  2. Automation of industrial bioprocesses.

    PubMed

    Beyeler, W; DaPra, E; Schneider, K

    2000-01-01

    The dramatic development of new electronic devices within the last 25 years has had a substantial influence on the control and automation of industrial bioprocesses. Within this short period of time the method of controlling industrial bioprocesses has changed completely. In this paper, the authors will use a practical approach focusing on the industrial applications of automation systems. From the early attempts to use computers for the automation of biotechnological processes up to the modern process automation systems some milestones are highlighted. Special attention is given to the influence of Standards and Guidelines on the development of automation systems.

  3. Shoe-String Automation

    SciTech Connect

    Duncan, M.L.

    2001-07-30

    Faced with a downsizing organization, serious budget reductions and retirement of key metrology personnel, maintaining capabilities to provide necessary services to our customers was becoming increasingly difficult. It appeared that the only solution was to automate some of our more personnel-intensive processes; however, it was crucial that the most personnel-intensive candidate process be automated, at the lowest price possible and with the lowest risk of failure. This discussion relates factors in the selection of the Standard Leak Calibration System for automation, the methods of automation used to provide the lowest-cost solution and the benefits realized as a result of the automation.

  4. Multistep generalized transformation method applied to solving equations of discrete and continuous time-fractional enzyme kinetics

    NASA Astrophysics Data System (ADS)

    Vosika, Z.; Mitić, V. V.; Vasić, A.; Lazović, G.; Matija, L.; Kocić, Lj. M.

    2017-03-01

    In this paper, Caputo based Michaelis-Menten kinetic model based on Time Scale Calculus (TSC) is proposed. The main reason for its consideration is a study of tumor cells population growth dynamics. In the particular case discrete-continuous time kinetics, Michaelis-Menten model is numerically treated, using a new algorithm proposed by authors, called multistep generalized difference transformation method (MSGDETM). In addition numerical simulations are performed and is shown that it represents the upgrade of the multi-step variant of generalized differential transformation method (MSGDTM). A possible conditions for its further development are discussed and possible experimental verification is described.

  5. A sandwich-type DNA electrochemical biosensor for hairpin-stem-loop structure based on multistep temperature-controlling method

    PubMed Central

    Hong, Guolin; Liu, Yinhuan; Chen, Wei; Weng, Shaohuang; Liu, Qicai; Liu, Ailin; Zheng, Daoxin; Lin, Xinhua

    2012-01-01

    A highly sensitive and selective method for amplified electrochemical detection for hairpin-stem-loop structured target sequences was developed based on the temperature regulation of DNA hybrids on a sandwich-type electrochemical DNA sensor. Multistep hybridization was applied to promote the hybridization efficiency of each section of sandwich structure. The results showed that both multistep and temperature-controlling hybridization techniques were both especially made to fabricate the sensor for the tendency of internal hybridization of target gene sequences. This strategy provides significantly enhanced hybridization efficiency and sequence specificity of electrochemical detection. PMID:23028223

  6. Multi-Step Bidirectional NDR Characteristics in Si/Si1-xGex/Si DHBTs and Their Temperature Dependence

    NASA Astrophysics Data System (ADS)

    Xu, D. X.; Shen, G. D.; Willander, M.; Hansson, G. V.

    1988-11-01

    Novel bidirectional negative differential resistance (NDR) phenomena have been observed at room temperature in strained base n-Si/p-Si1-xGex/n-Si double heterojunction bipolar transistors (DHBTs). A strong and symmetric bidirectional NDR modulated by base bias, together with a multi-step characteristic in collector current IC vs emitter-collector bias voltage VCE, was obtained in the devices with very thin base. The temperature dependence of the NDR and the multi-step IC-VCE characteristics has been measured to identify the possible transport mechanism. The physical origins of these phenomena are discussed.

  7. Molecular Analysis of a Multistep Lung Cancer Model Induced by Chronic Inflammation Reveals Epigenetic Regulation of p16 and Activation of the DNA Damage Response Pathway12

    PubMed Central

    Blanco, David; Vicent, Silvestre; Fraga, Mario F; Fernandez-Garcia, Ignacio; Freire, Javier; Lujambio, Amaia; Esteller, Manel; Ortiz-de-Solorzano, Carlos; Pio, Ruben; Lecanda, Fernando; Montuenga, Luis M

    2007-01-01

    The molecular hallmarks of inflammation-mediated lung carcinogenesis have not been fully clarified, mainly due to the scarcity of appropriate animal models. We have used a silica-induced multistep lung carcinogenesis model driven by chronic inflammation to study the evolution of molecular markers and genetic alterations. We analyzed markers of DNA damage response (DDR), proliferative stress, and telomeric stress: γ-H2AX, p16, p53, and TERT. Lung cancer-related epigenetic and genetic alterations, including promoter hypermethylation status of p16(CDKN2A), APC, CDH13, Rassf1, and Nore1A, as well as mutations of Tp53, epidermal growth factor receptor, K-ras, N-ras, and c-H-ras, have been also studied. Our results showed DDR pathway activation in preneoplastic lesions, in association with inducible nitric oxide synthase and p53 induction. p16 was also induced in early tumorigenic progression and was inactivated in bronchiolar dysplasias and tumors. Remarkably, lack of mutations of Ras and epidermal growth factor receptor, and a very low frequency of Tp53 mutations suggest that they are not required for tumorigenesis in this model. In contrast, epigenetic alterations in p16(CDKN2A), CDH13, and APC, but not in Rassf1 and Nore1A, were clearly observed. These data suggest the existence of a specific molecular signature of inflammation-driven lung carcinogenesis that shares some, but not all, of the molecular landmarks of chemically induced lung cancer. PMID:17971904

  8. Molecular analysis of a multistep lung cancer model induced by chronic inflammation reveals epigenetic regulation of p16 and activation of the DNA damage response pathway.

    PubMed

    Blanco, David; Vicent, Silvestre; Fraga, Mario F; Fernandez-Garcia, Ignacio; Freire, Javier; Lujambio, Amaia; Esteller, Manel; Ortiz-de-Solorzano, Carlos; Pio, Ruben; Lecanda, Fernando; Montuenga, Luis M

    2007-10-01

    The molecular hallmarks of inflammation-mediated lung carcinogenesis have not been fully clarified, mainly due to the scarcity of appropriate animal models. We have used a silica-induced multistep lung carcinogenesis model driven by chronic inflammation to study the evolution of molecular markers and genetic alterations. We analyzed markers of DNA damage response (DDR), proliferative stress, and telomeric stress: gamma-H2AX, p16, p53, and TERT. Lung cancer-related epigenetic and genetic alterations, including promoter hypermethylation status of p16(CDKN2A), APC, CDH13, Rassf1, and Nore1A, as well as mutations of Tp53, epidermal growth factor receptor, K-ras, N-ras, and c-H-ras, have been also studied. Our results showed DDR pathway activation in preneoplastic lesions, in association with inducible nitric oxide synthase and p53 induction. p16 was also induced in early tumorigenic progression and was inactivated in bronchiolar dysplasias and tumors. Remarkably, lack of mutations of Ras and epidermal growth factor receptor, and a very low frequency of Tp53 mutations suggest that they are not required for tumorigenesis in this model. In contrast, epigenetic alterations in p16(CDKN2A), CDH13, and APC, but not in Rassf1 and Nore1A, were clearly observed. These data suggest the existence of a specific molecular signature of inflammation-driven lung carcinogenesis that shares some, but not all, of the molecular landmarks of chemically induced lung cancer.

  9. Optimal multi-step collocation: application to the space-wise approach for GOCE data analysis

    NASA Astrophysics Data System (ADS)

    Reguzzoni, Mirko; Tselfes, Nikolaos

    2009-01-01

    Collocation is widely used in physical geodesy. Its application requires to solve systems with a dimension equal to the number of observations, causing numerical problems when many observations are available. To overcome this drawback, tailored step-wise techniques are usually applied. An example of these step-wise techniques is the space-wise approach to the GOCE mission data processing. The original idea of this approach was to implement a two-step procedure, which consists of first predicting gridded values at satellite altitude by collocation and then deriving the geo-potential spherical harmonic coefficients by numerical integration. The idea was generalized to a multi-step iterative procedure by introducing a time-wise Wiener filter to reduce the highly correlated observation noise. Recent studies have shown how to optimize the original two-step procedure, while the theoretical optimization of the full multi-step procedure is investigated in this work. An iterative operator is derived so that the final estimated spherical harmonic coefficients are optimal with respect to the Wiener-Kolmogorov principle, as if they were estimated by a direct collocation. The logical scheme used to derive this optimal operator can be applied not only in the case of the space-wise approach but, in general, for any case of step-wise collocation. Several numerical tests based on simulated realistic GOCE data are performed. The results show that adding a pre-processing time-wise filter to the two-step procedure of data gridding and spherical harmonic analysis is useful, in the sense that the accuracy of the estimated geo-potential coefficients is improved. This happens because, in its practical implementation, the gridding is made by collocation over local patches of data, while the observation noise has a time-correlation so long that it cannot be treated inside the patch size. Therefore, the multi-step operator, which is in theory equivalent to the two-step operator and to the

  10. Automated DNA Sequencing System

    SciTech Connect

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  11. Automated Design of Quantum Circuits

    NASA Technical Reports Server (NTRS)

    Williams, Colin P.; Gray, Alexander G.

    2000-01-01

    In order to design a quantum circuit that performs a desired quantum computation, it is necessary to find a decomposition of the unitary matrix that represents that computation in terms of a sequence of quantum gate operations. To date, such designs have either been found by hand or by exhaustive enumeration of all possible circuit topologies. In this paper we propose an automated approach to quantum circuit design using search heuristics based on principles abstracted from evolutionary genetics, i.e. using a genetic programming algorithm adapted specially for this problem. We demonstrate the method on the task of discovering quantum circuit designs for quantum teleportation. We show that to find a given known circuit design (one which was hand-crafted by a human), the method considers roughly an order of magnitude fewer designs than naive enumeration. In addition, the method finds novel circuit designs superior to those previously known.

  12. Variation of nanopore diameter along porous anodic alumina channels by multi-step anodization.

    PubMed

    Lee, Kwang Hong; Lim, Xin Yuan; Wai, Kah Wing; Romanato, Filippo; Wong, Chee Cheong

    2011-02-01

    In order to form tapered nanocapillaries, we investigated a method to vary the nanopore diameter along the porous anodic alumina (PAA) channels using multi-step anodization. By anodizing the aluminum in either single acid (H3PO4) or multi-acid (H2SO4, oxalic acid and H3PO4) with increasing or decreasing voltage, the diameter of the nanopore along the PAA channel can be varied systematically corresponding to the applied voltages. The pore size along the channel can be enlarged or shrunken in the range of 20 nm to 200 nm. Structural engineering of the template along the film growth direction can be achieved by deliberately designing a suitable voltage and electrolyte together with anodization time.

  13. Numerical multistep methods for the efficient solution of quantum mechanics and related problems

    NASA Astrophysics Data System (ADS)

    Anastassi, Z. A.; Simos, T. E.

    2009-10-01

    In this paper we present the recent development in the numerical integration of the Schrödinger equation and related systems of ordinary differential equations with oscillatory solutions, such as the N-body problem. We examine several types of multistep methods (explicit, implicit, predictor-corrector, hybrid) and several properties (P-stability, trigonometric fitting of various orders, phase fitting, high phase-lag order, algebraic order). We analyze the local truncation error and the stability of the methods. The error for the Schrödinger equation is also presented, which reveals the relation of the error to the energy. The efficiency of the methods is evaluated through the integration of five problems. Figures are presented and analyzed and some general conclusions are made. Code written in Maple is given for the development of all methods analyzed in this paper. Also the subroutines written in Matlab, that concern the integration of the methods, are presented.

  14. A multistep ac electrodeposition method to prepare Co nanowires with high coercivity

    NASA Astrophysics Data System (ADS)

    Wang, Pangpang; Gao, Lumei; Qiu, Zhiyong; Song, Xiaoping; Wang, Liqun; Yang, Sen; Murakami, Ri-ichi

    2008-09-01

    It is known that the ac electrodeposition method with low current density can grow compact metal nanowires, but the length of those nanowires is very short. In contrast, the ac electrodeposition method with high current density can grow long metal nanowires. However these long nanowires are not compact and contain lots of defects. In this paper, we describe a multistep ac electrodeposition method to fabricate long metal nanowires with compact structure uniformly filled upon a porous anodic aluminum oxide template. Using this method, Co nanowires with high coercivity (Hc ∥) and remnant ratio (Mr/Ms) have been prepared under relatively low deposition current density. The Co nanowires exhibited obvious magnetic anisotropy with the easy axis along the axial direction of nanowires. The maximal Hc ∥ (2900 Oe) and Mr/Ms (0.95) were optimal for the perpendicular magnetic recording materials. The magnetic microstructure of Co nanowires is also discussed in this paper.

  15. Conjugate symplecticity of second-order linear multi-step methods

    NASA Astrophysics Data System (ADS)

    Feng, Quan-Dong; Jiao, Yan-Dong; Tang, Yi-Fa

    2007-06-01

    We review the two different approaches for symplecticity of linear multi-step methods (LMSM) by Eirola and Sanz-Serna, Ge and Feng, and by Feng and Tang, Hairer and Leone, respectively, and give a numerical example between these two approaches. We prove that in the conjugate relation with and being LMSMs, if is symplectic, then the B-series error expansions of , and of the form are equal to those of trapezoid, mid-point and Euler forward schemes up to a parameter [theta] (completely the same when [theta]=1), respectively, this also partially solves a problem due to Hairer. In particular we indicate that the second-order symmetric leap-frog scheme Z2=Z0+2[tau]J-1[backward difference]H(Z1) cannot be conjugate-symplectic via another LMSM.

  16. A multistep game of kind between two economic systems under complete information

    SciTech Connect

    Malyukov, V.P.; Linder, N.V.

    1995-03-01

    We consider the problem of conflict interaction between two economic systems described by Leontief type single-commodity dynamic models. The problem is solved in the framework of a positional multistep game of kind under complete information assuming several terminal sets. The solution constructs optimality sets of the players that control the dynamic models and finds the winning strategies. As in the analysis of related games, the solution of the problem is found to depend on the relationship of the parameters that define the conflict interaction. Contrary to, our study does not assume nonnegativity of some of the game parameters. The solution is obtained for all possible relationships of game parameters; examples of a conflict interaction in dynamic economic models are given.

  17. Structure of magnesium alloy MA14 after multistep isothermal forging and subsequent isothermal rolling

    NASA Astrophysics Data System (ADS)

    Nugmanov, D. R.; Sitdikov, O. Sh.; Markushev, M. V.

    2015-10-01

    Optical metallography and electron microscopy have been used to analyze the structural changes in magnesium MA14 alloy subjected to processing that combines multistep isothermal forging and isothermal rolling. It has been found that forging of a bulk workpiece leads to the formation of a structure, 85-90% of which consists of recrystallized grains with an average size of less than 5 µm. Subsequent rolling results in a completely recrystallized structure with a grain size of 1-2 µm. It is shown that the resultant structural states are characterized by grain size nonuniformity inherited from the initial hot-pressed semi-finished product. The nature and features of crystallization processes that take place in the alloy during processing are discussed.

  18. Quantum preequilibrium multistep direct calculations for nucleon scattering on deformed nuclei: a microscopic approach

    NASA Astrophysics Data System (ADS)

    Dupuis, Marc; Bonneau, Ludovic; Kawano, Toshihiko

    2008-04-01

    An introduction of the different quantum mechanics models is given for the calculation of pre-equilibrium multistep direct process for nucleon induced reaction. A practical application is presented for 238U neutron induced reaction at medium energy (10-20 MeV). The double differential cross-sections are calculated with no adjustable parameter and reproduced the data very well. The cross-sections are expressed as a sum of DWBA transition amplitudes computed with a microscopic two-body interaction. The exited states of the target are expressed as particle-hole excitations built from single particle states obtained with the HF+BCS calculation with a Skyrme force. We also perform a sensitivity study our calculations with respect to the ingredients of the model, namely the two-body interaction which generates the transitions and the target states description.

  19. A multistep photothermic-driven drug release system using wire-framed Au nanobundles.

    PubMed

    Bang, Doyeon; Lee, Taeksu; Choi, Jihye; Park, Yeonji; Kim, Eunkyoung; Huh, Yong-Min; Haam, Seungjoo

    2015-01-28

    Here, wire-framed Au nanobundles (WNBs), which consist of randomly oriented and mutually connected Au wires to form a bundle shape, are synthesized. In contrast to conventional nanoparticles (spheres, rods, cubes, and stars), which exhibit nanostructure only on the surface, cross-sectional view image shows that WNBs have nanostructures in a whole volume. By using this specific property of WNBs, an externally controllable multistep photothermic-driven drug release (PDR) system is demonstrated for in vivo cancer treatment. In contrast to conventional nanoparticles that encapsulate a drug on their surface, WNBs preserve the drug payload in the overall inner volume, providing a drug loading capacity sufficient for cancer therapy. An improved in vivo therapeutic efficacy of PDR therapy is also demonstrated by delivering sufficient amount of drugs to the target tumor region.

  20. Multistep divergent synthesis of benzimidazole linked benzoxazole/benzothiazole via copper catalyzed domino annulation.

    PubMed

    Liao, Jen-Yu; Selvaraju, Manikandan; Chen, Chih-Hau; Sun, Chung-Ming

    2013-04-21

    An efficient, facile synthesis of structurally diverse benzimidazole integrated benzoxazole and benzothiazoles has been developed. In a multi-step synthetic sequence, 4-fluoro-3-nitrobenzoic acid was converted into benzimidazole bis-heterocycles, via the intermediacy of benzimidazole linked ortho-chloro amines. The amphiphilic reactivity of this intermediate was designed to achieve the title compounds by the reaction of various acid chlorides and isothiocyanates in a single step through the in situ formation of ortho-chloro anilides and thioureas under microwave irradiation. A versatile one pot domino annulation reaction was developed to involve the reaction of benzimidazole linked ortho-chloro amines with acid chlorides and isothiocyanates. The initial acylation and urea formation followed by copper catalyzed intramolecular C-O and C-S cross coupling reactions furnished the angularly oriented bis-heterocycles which bear a close resemblance to the streptomyces antibiotic UK-1.

  1. The solution of Parrondo’s games with multi-step jumps

    NASA Astrophysics Data System (ADS)

    Saakian, David B.

    2016-04-01

    We consider the general case of Parrondo’s games, when there is a finite probability to stay in the current state as well as multi-step jumps. We introduce a modification of the model: the transition probabilities between different games depend on the choice of the game in the previous round. We calculate the rate of capital growth as well as the variance of the distribution, following large deviation theory. The modified model allows higher capital growth rates than in standard Parrondo games for the range of parameters considered in the key articles about these games, and positive capital growth is possible for a much wider regime of parameters of the model.

  2. Semi-Lagrangian multistep exponential integrators for index 2 differential-algebraic systems

    NASA Astrophysics Data System (ADS)

    Celledoni, Elena; Kometa, Bawfeh Kingsley

    2011-05-01

    Implicit-explicit (IMEX) multistep methods are very useful for the time discretization of convection diffusion PDE problems such as the Burgers equations and the incompressible Navier-Stokes equations. In the latter as well as in PDE models of plasma physics and of electromechanical systems, semi-discretization in space gives rise to differential-algebraic (DAE) system of equations often of index higher than 1. In this paper we propose a new class of exponential integrators for index 2 DAEs arising from the semi-discretization of PDEs with a dominating and typically nonlinear convection term. This class of problems includes the incompressible Navier-Stokes equations. The integration methods are based on the backward differentiation formulae (BDF) and they can be applied without modifications in the semi-Lagrangian integration of convection diffusion problems. The approach gives improved performance at low viscosity regimes.

  3. Continuous Synthesis and Purification by Coupling a Multistep Flow Reaction with Centrifugal Partition Chromatography.

    PubMed

    Örkényi, Róbert; Éles, János; Faigl, Ferenc; Vincze, Péter; Prechl, Anita; Szakács, Zoltán; Kóti, János; Greiner, István

    2017-07-17

    Continuous-flow multistep synthesis is combined with quasi-continuous final-product purification to produce pure products from crude reaction mixtures. In the nucleophilic aromatic substitution of 2,4-difluoronitrobenzene with morpholine followed by a heterogeneous catalytic hydrogenation, the desired monosubstituted product can be continuously separated from the co- and by-products in a purity of over 99 % by coupling a flow reactor sequence to a multiple dual-mode (MDM) centrifugal partition chromatography (CPC) device. This purification technique has many advantages over HPLC, such as higher resolution and no need for column replacement or silica recycling, and it does not suffer from irreversible adsorption. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  4. The route from problem to solution in multistep continuous flow synthesis of pharmaceutical compounds.

    PubMed

    Bana, Péter; Örkényi, Róbert; Lövei, Klára; Lakó, Ágnes; Túrós, György István; Éles, János; Faigl, Ferenc; Greiner, István

    2016-12-29

    Recent advances in the field of continuous flow chemistry allow the multistep preparation of complex molecules such as APIs (Active Pharmaceutical Ingredients) in a telescoped manner. Numerous examples of laboratory-scale applications are described, which are pointing towards novel manufacturing processes of pharmaceutical compounds, in accordance with recent regulatory, economical and quality guidances. The chemical and technical knowledge gained during these studies is considerable; nevertheless, connecting several individual chemical transformations and the attached analytics and purification holds hidden traps. In this review, we summarize innovative solutions for these challenges, in order to benefit chemists aiming to exploit flow chemistry systems for the synthesis of biologically active molecules. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Multistep modeling of protein structure: application towards refinement of tyr-tRNA synthetase

    NASA Technical Reports Server (NTRS)

    Srinivasan, S.; Shibata, M.; Roychoudhury, M.; Rein, R.

    1987-01-01

    The scope of multistep modeling (MSM) is expanding by adding a least-squares minimization step in the procedure to fit backbone reconstruction consistent with a set of C-alpha coordinates. The analytical solution of Phi and Psi angles, that fits a C-alpha x-ray coordinate is used for tyr-tRNA synthetase. Phi and Psi angles for the region where the above mentioned method fails, are obtained by minimizing the difference in C-alpha distances between the computed model and the crystal structure in a least-squares sense. We present a stepwise application of this part of MSM to the determination of the complete backbone geometry of the 321 N terminal residues of tyrosine tRNA synthetase to a root mean square deviation of 0.47 angstroms from the crystallographic C-alpha coordinates.

  6. Real-Time Multi-Step View Reconstruction for a Virtual Teleconference System

    NASA Astrophysics Data System (ADS)

    Lei, B. J.; Hendriks, E. A.

    2002-12-01

    We propose a real-time multi-step view reconstruction algorithm and we tune its implementation to a virtual teleconference application. Theoretical motivations and practical implementation issues of the algorithm are detailed. The proposed algorithm can be used to reconstruct novel views at arbitrary poses (position and orientation) in a way that is geometrically valid. The algorithm is applied to a virtual teleconference system. In this system, we show that it can provide high-quality nearby virtual views that are comparable with the real perceived view. We experimentally show that, due to the modular approach, a real-time implementation is feasible. Finally, it is proved that it is possible to seamlessly integrate the proposed view reconstruction approach with other parts of the teleconference system. This integration can speed up the virtual view reconstruction.

  7. Controlled growth of SnO(2) hierarchical nanostructures by a multistep thermal vapor deposition process.

    PubMed

    Sun, Shuhui; Meng, Guowen; Zhang, Gaixia; Masse, Jean-Philippe; Zhang, Lide

    2007-01-01

    Branched and sub-branched SnO(2) hierarchical architectures in which numerous aligned nanowires grew on the surface of nanobelt substrates have been obtained by a multistep thermal vapor deposition route. Branch size and morphology can be controlled by adjusting the temperature and duration of growth. The same approach was used to grow branched ZnO-SnO(2) heterojunction nanostructures. In addition, the third level of SnO(2) nanostructures was obtained by repeating the vapor deposition growth process. This technique provides a general, facile, and convenient approach for preparing even more complex nanoarchitectures, and should open up new opportunities for both fundamental research and applications, such as nanobelt-based three-dimensional nanodevices.

  8. A Multi-Step Assessment Scheme for Seismic Network Site Selection in Densely Populated Areas

    NASA Astrophysics Data System (ADS)

    Plenkers, Katrin; Husen, Stephan; Kraft, Toni

    2015-10-01

    We developed a multi-step assessment scheme for improved site selection during seismic network installation in densely populated areas. Site selection is a complex process where different aspects (seismic background noise, geology, and financing) have to be taken into account. In order to improve this process, we developed a step-wise approach that allows quantifying the quality of a site by using, in addition to expert judgement and test measurements, two weighting functions as well as reference stations. Our approach ensures that the recording quality aimed for is reached and makes different sites quantitatively comparable to each other. Last but not least, it is an easy way to document the decision process, because all relevant parameters are listed, quantified, and weighted.

  9. Multistep modeling of protein structure: application towards refinement of tyr-tRNA synthetase

    NASA Technical Reports Server (NTRS)

    Srinivasan, S.; Shibata, M.; Roychoudhury, M.; Rein, R.

    1987-01-01

    The scope of multistep modeling (MSM) is expanding by adding a least-squares minimization step in the procedure to fit backbone reconstruction consistent with a set of C-alpha coordinates. The analytical solution of Phi and Psi angles, that fits a C-alpha x-ray coordinate is used for tyr-tRNA synthetase. Phi and Psi angles for the region where the above mentioned method fails, are obtained by minimizing the difference in C-alpha distances between the computed model and the crystal structure in a least-squares sense. We present a stepwise application of this part of MSM to the determination of the complete backbone geometry of the 321 N terminal residues of tyrosine tRNA synthetase to a root mean square deviation of 0.47 angstroms from the crystallographic C-alpha coordinates.

  10. Quantum preequilibrium multistep direct calculations for nucleon scattering on deformed nuclei: a microscopic approach

    SciTech Connect

    Dupuis, Marc; Kawano, Toshihiko; Bonneau, Ludovic

    2008-04-17

    An introduction of the different quantum mechanics models is given for the calculation of pre-equilibrium multistep direct process for nucleon induced reaction. A practical application is presented for {sup 238}U neutron induced reaction at medium energy (10-20 MeV). The double differential cross-sections are calculated with no adjustable parameter and reproduced the data very well. The cross-sections are expressed as a sum of DWBA transition amplitudes computed with a microscopic two-body interaction. The exited states of the target are expressed as particle-hole excitations built from single particle states obtained with the HF+BCS calculation with a Skyrme force. We also perform a sensitivity study our calculations with respect to the ingredients of the model, namely the two-body interaction which generates the transitions and the target states description.

  11. Automated measurement of zebrafish larval movement

    PubMed Central

    Cario, Clinton L; Farrell, Thomas C; Milanese, Chiara; Burton, Edward A

    2011-01-01

    Abstract The zebrafish is a powerful vertebrate model that is readily amenable to genetic, pharmacological and environmental manipulations to elucidate the molecular and cellular basis of movement and behaviour. We report software enabling automated analysis of zebrafish movement from video recordings captured with cameras ranging from a basic camcorder to more specialized equipment. The software, which is provided as open-source MATLAB functions, can be freely modified and distributed, and is compatible with multiwell plates under a wide range of experimental conditions. Automated measurement of zebrafish movement using this technique will be useful for multiple applications in neuroscience, pharmacology and neuropsychiatry. PMID:21646414

  12. Dynamical genetic programming in XCSF.

    PubMed

    Preen, Richard J; Bull, Larry

    2013-01-01

    A number of representation schemes have been presented for use within learning classifier systems, ranging from binary encodings to artificial neural networks. This paper presents results from an investigation into using a temporally dynamic symbolic representation within the XCSF learning classifier system. In particular, dynamical arithmetic networks are used to represent the traditional condition-action production system rules to solve continuous-valued reinforcement learning problems and to perform symbolic regression, finding competitive performance with traditional genetic programming on a number of composite polynomial tasks. In addition, the network outputs are later repeatedly sampled at varying temporal intervals to perform multistep-ahead predictions of a financial time series.

  13. A multistep approach to single nucleotide polymorphism-set analysis: an evaluation of power and type I error of gene-based tests of association after pathway-based association tests.

    PubMed

    Valcarcel, Alessandra; Grinde, Kelsey; Cook, Kaitlyn; Green, Alden; Tintle, Nathan

    2016-01-01

    The aggregation of functionally associated variants given a priori biological information can aid in the discovery of rare variants associated with complex diseases. Many methods exist that aggregate rare variants into a set and compute a single p value summarizing association between the set of rare variants and a phenotype of interest. These methods are often called gene-based, rare variant tests of association because the variants in the set are often all contained within the same gene. A reasonable extension of these approaches involves aggregating variants across an even larger set of variants (eg, all variants contained in genes within a pathway). Testing sets of variants such as pathways for association with a disease phenotype reduces multiple testing penalties, may increase power, and allows for straightforward biological interpretation. However, a significant variant-set association test does not indicate precisely which variants contained within that set are causal. Because pathways often contain many variants, it may be helpful to follow-up significant pathway tests by conducting gene-based tests on each gene in that pathway to narrow in on the region of causal variants. In this paper, we propose such a multistep approach for variant-set analysis that can also account for covariates and complex pedigree structure. We demonstrate this approach on simulated phenotypes from Genetic Analysis Workshop 19. We find generally better power for the multistep approach when compared to a more conventional, single-step approach that simply runs gene-based tests of association on each gene across the genome. Further work is necessary to evaluate the multistep approach on different data sets with different characteristics.

  14. Continuous multistep synthesis of perillic acid from limonene by catalytic biofilms under segmented flow.

    PubMed

    Willrodt, Christian; Halan, Babu; Karthaus, Lisa; Rehdorf, Jessica; Julsing, Mattijs K; Buehler, Katja; Schmid, Andreas

    2017-02-01

    The efficiency of biocatalytic reactions involving industrially interesting reactants is often constrained by toxification of the applied biocatalyst. Here, we evaluated the combination of biologically and technologically inspired strategies to overcome toxicity-related issues during the multistep oxyfunctionalization of (R)-(+)-limonene to (R)-(+)-perillic acid. Pseudomonas putida GS1 catalyzing selective limonene oxidation via the p-cymene degradation pathway and recombinant Pseudomonas taiwanensis VLB120 were evaluated for continuous perillic acid production. A tubular segmented-flow biofilm reactor was used in order to relieve oxygen limitations and to enable membrane mediated substrate supply as well as efficient in situ product removal. Both P. putida GS1 and P. taiwanensis VLB120 developed a catalytic biofilm in this system. The productivity of wild-type P. putida GS1 encoding the enzymes for limonene bioconversion was highly dependent on the carbon source and reached 34 g Ltube(-1)  day(-1) when glycerol was supplied. More than 10-fold lower productivities were reached irrespective of the applied carbon source when the recombinant P. taiwanensis VLB120 harboring p-cymene monooxygenase and p-cumic alcohol dehydrogenase was used as biocatalyst. The technical applicability for preparative perillic acid synthesis in the applied system was verified by purification of perillic acid from the outlet stream using an anion exchanger resin. This concept enabled the multistep production of perillic acid and which might be transferred to other reactions involving volatile reactants and toxic end-products. Biotechnol. Bioeng. 2017;114: 281-290. © 2016 Wiley Periodicals, Inc.

  15. Progressive Enrichment of Stemness Features and Tumor Stromal Alterations in Multistep Hepatocarcinogenesis.

    PubMed

    Yoo, Jeong Eun; Kim, Young-Joo; Rhee, Hyungjin; Kim, Haeryoung; Ahn, Ei Yong; Choi, Jin Sub; Roncalli, Massimo; Park, Young Nyun

    2017-01-01

    Cancer stem cells (CSCs), a subset of tumor cells, contribute to an aggressive biological behavior, which is also affected by the tumor stroma. Despite the role of CSCs and the tumor stroma in hepatocellular carcinoma (HCC), features of stemness have not yet been studied in relation to tumor stromal alterations in multistep hepatocarcinogenesis. We investigated the expression status of stemness markers and tumor stromal changes in B viral carcinogenesis, which is the main etiology of HCC in Asia. Stemness features of tumoral hepatocytes (EpCAM, K19, Oct3/4, c-KIT, c-MET, and CD133), and tumor stromal cells expressing α-smooth muscle actin (α-SMA), CD68, CD163, and IL-6 were analyzed in 36 low grade dysplastic nodules (DNs), 48 high grade DNs, 30 early HCCs (eHCCs), and 51 progressed HCCs (pHCCs) by immunohistochemistry or real-time PCR. Stemness features (EpCAM and K19 in particular) were progressively acquired during hepatocarcinogenesis in combination with enrichment of stromal cells (CAFs, TAMs, IL-6+ cells). Stemness features were seen sporadically in DNs, more consistent in eHCCs, and peaked in pHCCs. Likewise, stromal cells were discernable in DNs, showed up as consistent cell densities in eHCCs and peaked in pHCCs. The stemness features and tumor stromal alterations also peaked in less differentiated or larger HCCs. In conclusion, progression of B viral multistep hepatocarcinogenesis is characterized by an enrichment of stemness features of neoplastic hepatocytes and a parallel alteration of the tumor stroma. The modulation of neoplastic hepatocytes and stromal cells was at low levels in precancerous lesions (DNs), consistently increased in incipient cancer (eHCCs) and peaked in pHCCs. Thus, in B viral hepatocarcinogenesis, interactions between CSCs and the tumor stroma, although starting early, seem to play a major role in tumor progression.

  16. Multicomponent and multistep radioactive decay modeling module for groundwater flow and contaminant transport computer code

    NASA Astrophysics Data System (ADS)

    Kharkhordin, I. L.

    2013-12-01

    Correct calculations of multistep radioactive decay is important for radionuclide transport forecast at contaminated sites and designing radionuclide storage facilities as well as for a number applications of natural radioactive tracers for understanding of groundwater flow in complex hydrogeological systems. Radioactive chains can involves a number of branches with certain probabilities of decay and up to fourteen steps. General description of radioactive decay in complex system could be presented as a system of linear differential equations. Numerical solution of this system encounters a difficulties connected with wide rage of radioactive decay constants variations. In present work the database with 1253 records of radioactive isotope decay parameters for 97 elements was created. An algorithm of analytical solution construction and solving was elaborated for arbitrary radioactive isotope system taking into account the possible chain branching and connection. The algorithm is based on radionuclide decay graphs. The main steps of algorithm is as follows: a) searching of all possible isotopes in database, creation full isotope list; b) looking for main parent isotopes; c) construction of all possible radioactive chains; d) looking for branching and connections in decay chains, marking of links as primary (left chain in graph for main parent isotope), secondary (after connection), and recurring (before branching); e) construction and calculation the coefficients for analytical solutions. The developed computer code was tested on a few simple systems like follows: Cs-135 - one step decay, Sr-90 (Y-90) - two steps decay, U-238+U-235 mixture - complex decay with branching. Calculation of radiogenic He-4 is also possible witch could be important application for groundwater flow and transport model calibration using natural tracers. The computer code for multistep radioactive calculation was elaborated for incorporation into NIMFA code. NIMFA is a parallel computer code

  17. Progressive Enrichment of Stemness Features and Tumor Stromal Alterations in Multistep Hepatocarcinogenesis

    PubMed Central

    Rhee, Hyungjin; Kim, Haeryoung; Ahn, Ei Yong; Choi, Jin Sub; Roncalli, Massimo; Park, Young Nyun

    2017-01-01

    Cancer stem cells (CSCs), a subset of tumor cells, contribute to an aggressive biological behavior, which is also affected by the tumor stroma. Despite the role of CSCs and the tumor stroma in hepatocellular carcinoma (HCC), features of stemness have not yet been studied in relation to tumor stromal alterations in multistep hepatocarcinogenesis. We investigated the expression status of stemness markers and tumor stromal changes in B viral carcinogenesis, which is the main etiology of HCC in Asia. Stemness features of tumoral hepatocytes (EpCAM, K19, Oct3/4, c-KIT, c-MET, and CD133), and tumor stromal cells expressing α-smooth muscle actin (α-SMA), CD68, CD163, and IL-6 were analyzed in 36 low grade dysplastic nodules (DNs), 48 high grade DNs, 30 early HCCs (eHCCs), and 51 progressed HCCs (pHCCs) by immunohistochemistry or real-time PCR. Stemness features (EpCAM and K19 in particular) were progressively acquired during hepatocarcinogenesis in combination with enrichment of stromal cells (CAFs, TAMs, IL-6+ cells). Stemness features were seen sporadically in DNs, more consistent in eHCCs, and peaked in pHCCs. Likewise, stromal cells were discernable in DNs, showed up as consistent cell densities in eHCCs and peaked in pHCCs. The stemness features and tumor stromal alterations also peaked in less differentiated or larger HCCs. In conclusion, progression of B viral multistep hepatocarcinogenesis is characterized by an enrichment of stemness features of neoplastic hepatocytes and a parallel alteration of the tumor stroma. The modulation of neoplastic hepatocytes and stromal cells was at low levels in precancerous lesions (DNs), consistently increased in incipient cancer (eHCCs) and peaked in pHCCs. Thus, in B viral hepatocarcinogenesis, interactions between CSCs and the tumor stroma, although starting early, seem to play a major role in tumor progression. PMID:28114366

  18. Cross-cultural adaptation of instruments assessing breastfeeding determinants: a multi-step approach

    PubMed Central

    2014-01-01

    Background Cross-cultural adaptation is a necessary process to effectively use existing instruments in other cultural and language settings. The process of cross-culturally adapting, including translation, of existing instruments is considered a critical set to establishing a meaningful instrument for use in another setting. Using a multi-step approach is considered best practice in achieving cultural and semantic equivalence of the adapted version. We aimed to ensure the content validity of our instruments in the cultural context of KwaZulu-Natal, South Africa. Methods The Iowa Infant Feeding Attitudes Scale, Breastfeeding Self-Efficacy Scale-Short Form and additional items comprise our consolidated instrument, which was cross-culturally adapted utilizing a multi-step approach during August 2012. Cross-cultural adaptation was achieved through steps to maintain content validity and attain semantic equivalence in the target version. Specifically, Lynn’s recommendation to apply an item-level content validity index score was followed. The revised instrument was translated and back-translated. To ensure semantic equivalence, Brislin’s back-translation approach was utilized followed by the committee review to address any discrepancies that emerged from translation. Results Our consolidated instrument was adapted to be culturally relevant and translated to yield more reliable and valid results for use in our larger research study to measure infant feeding determinants effectively in our target cultural context. Conclusions Undertaking rigorous steps to effectively ensure cross-cultural adaptation increases our confidence that the conclusions we make based on our self-report instrument(s) will be stronger. In this way, our aim to achieve strong cross-cultural adaptation of our consolidated instruments was achieved while also providing a clear framework for other researchers choosing to utilize existing instruments for work in other cultural, geographic and population

  19. A Dimensionality Reduction-Based Multi-Step Clustering Method for Robust Vessel Trajectory Analysis.

    PubMed

    Li, Huanhuan; Liu, Jingxian; Liu, Ryan Wen; Xiong, Naixue; Wu, Kefeng; Kim, Tai-Hoon

    2017-08-04

    The Shipboard Automatic Identification System (AIS) is crucial for navigation safety and maritime surveillance, data mining and pattern analysis of AIS information have attracted considerable attention in terms of both basic research and practical applications. Clustering of spatio-temporal AIS trajectories can be used to identify abnormal patterns and mine customary route data for transportation safety. Thus, the capacities of navigation safety and maritime traffic monitoring could be enhanced correspondingly. However, trajectory clustering is often sensitive to undesirable outliers and is essentially more complex compared with traditional point clustering. To overcome this limitation, a multi-step trajectory clustering method is proposed in this paper for robust AIS trajectory clustering. In particular, the Dynamic Time Warping (DTW), a similarity measurement method, is introduced in the first step to measure the distances between different trajectories. The calculated distances, inversely proportional to the similarities, constitute a distance matrix in the second step. Furthermore, as a widely-used dimensional reduction method, Principal Component Analysis (PCA) is exploited to decompose the obtained distance matrix. In particular, the top k principal components with above 95% accumulative contribution rate are extracted by PCA, and the number of the centers k is chosen. The k centers are found by the improved center automatically selection algorithm. In the last step, the improved center clustering algorithm with k clusters is implemented on the distance matrix to achieve the final AIS trajectory clustering results. In order to improve the accuracy of the proposed multi-step clustering algorithm, an automatic algorithm for choosing the k clusters is developed according to the similarity distance. Numerous experiments on realistic AIS trajectory datasets in the bridge area waterway and Mississippi River have been implemented to compare our proposed method with

  20. A Dimensionality Reduction-Based Multi-Step Clustering Method for Robust Vessel Trajectory Analysis

    PubMed Central

    Liu, Jingxian; Wu, Kefeng

    2017-01-01

    The Shipboard Automatic Identification System (AIS) is crucial for navigation safety and maritime surveillance, data mining and pattern analysis of AIS information have attracted considerable attention in terms of both basic research and practical applications. Clustering of spatio-temporal AIS trajectories can be used to identify abnormal patterns and mine customary route data for transportation safety. Thus, the capacities of navigation safety and maritime traffic monitoring could be enhanced correspondingly. However, trajectory clustering is often sensitive to undesirable outliers and is essentially more complex compared with traditional point clustering. To overcome this limitation, a multi-step trajectory clustering method is proposed in this paper for robust AIS trajectory clustering. In particular, the Dynamic Time Warping (DTW), a similarity measurement method, is introduced in the first step to measure the distances between different trajectories. The calculated distances, inversely proportional to the similarities, constitute a distance matrix in the second step. Furthermore, as a widely-used dimensional reduction method, Principal Component Analysis (PCA) is exploited to decompose the obtained distance matrix. In particular, the top k principal components with above 95% accumulative contribution rate are extracted by PCA, and the number of the centers k is chosen. The k centers are found by the improved center automatically selection algorithm. In the last step, the improved center clustering algorithm with k clusters is implemented on the distance matrix to achieve the final AIS trajectory clustering results. In order to improve the accuracy of the proposed multi-step clustering algorithm, an automatic algorithm for choosing the k clusters is developed according to the similarity distance. Numerous experiments on realistic AIS trajectory datasets in the bridge area waterway and Mississippi River have been implemented to compare our proposed method with

  1. Star sub-pixel centroid calculation based on multi-step minimum energy difference method

    NASA Astrophysics Data System (ADS)

    Wang, Duo; Han, YanLi; Sun, Tengfei

    2013-09-01

    The star's centroid plays a vital role in celestial navigation, star images which be gotten during daytime, due to the strong sky background, have a low SNR, and the star objectives are nearly submerged in the background, takes a great trouble to the centroid localization. Traditional methods, such as a moment method, weighted centroid calculation method is simple but has a big error, especially in the condition of a low SNR. Gaussian method has a high positioning accuracy, but the computational complexity. Analysis of the energy distribution in star image, a location method for star target centroids based on multi-step minimum energy difference is proposed. This method uses the linear superposition to narrow the centroid area, in the certain narrow area uses a certain number of interpolation to pixels for the pixels' segmentation, and then using the symmetry of the stellar energy distribution, tentatively to get the centroid position: assume that the current pixel is the star centroid position, and then calculates and gets the difference of the sum of the energy which in the symmetric direction(in this paper we take the two directions of transverse and longitudinal) and the equal step length(which can be decided through different conditions, the paper takes 9 as the step length) of the current pixel, and obtain the centroid position in this direction when the minimum difference appears, and so do the other directions, then the validation comparison of simulated star images, and compare with several traditional methods, experiments shows that the positioning accuracy of the method up to 0.001 pixel, has good effect to calculate the centroid of low SNR conditions; at the same time, uses this method on a star map which got at the fixed observation site during daytime in near-infrared band, compare the results of the paper's method with the position messages which were known of the star, it shows that :the multi-step minimum energy difference method achieves a better

  2. Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer

    PubMed Central

    2010-01-01

    Background The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations. Results Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aβ-binding or cathepsin E-inhibition. Conclusions With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-μL scale have become possible. PMID:20923572

  3. Synthesis of Frontalin, the Aggregation Pheromone of the Southern Pine Beetle: A Multistep Organic Synthesis for Undergraduate Students.

    ERIC Educational Resources Information Center

    Bartlett, Paul A.; And Others

    1984-01-01

    Background information and experimental procedures are provided for the multistep synthesis of frontalin. The experiment exposes students to a range of practical laboratory problems and important synthetic reactions and provides experiences in working on a medium-size, as well as a relatively small-size scale. (JN)

  4. Synthesis of 10-Ethyl Flavin: A Multistep Synthesis Organic Chemistry Laboratory Experiment for Upper-Division Undergraduate Students

    ERIC Educational Resources Information Center

    Sichula, Vincent A.

    2015-01-01

    A multistep synthesis of 10-ethyl flavin was developed as an organic chemistry laboratory experiment for upper-division undergraduate students. Students synthesize 10-ethyl flavin as a bright yellow solid via a five-step sequence. The experiment introduces students to various hands-on experimental organic synthetic techniques, such as column…

  5. A Multistep Organocatalysis Experiment for the Undergraduate Organic Laboratory: An Enantioselective Aldol Reaction Catalyzed by Methyl Prolinamide

    ERIC Educational Resources Information Center

    Wade, Edmir O.; Walsh, Kenneth E.

    2011-01-01

    In recent years, there has been an explosion of research concerning the area of organocatalysis. A multistep capstone laboratory project that combines traditional reactions frequently found in organic laboratory curriculums with this new field of research is described. In this experiment, the students synthesize a prolinamide-based organocatalyst…

  6. Synthesis of Two Local Anesthetics from Toluene: An Organic Multistep Synthesis in a Project-Oriented Laboratory Course

    ERIC Educational Resources Information Center

    Demare, Patricia; Regla, Ignacio

    2012-01-01

    This article describes one of the projects in the advanced undergraduate organic chemistry laboratory course concerning the synthesis of two local anesthetic drugs, prilocaine and benzocaine, with a common three-step sequence starting from toluene. Students undertake, in a several-week independent project, the multistep synthesis of a…

  7. Multistep soft chemistry method for valence reduction in transition metal oxides with triangular (CdI2-type) layers.

    PubMed

    Blakely, Colin K; Bruno, Shaun R; Poltavets, Viktor V

    2014-03-14

    Transition metal (M) oxides with MO2 triangular layers demonstrate a variety of physical properties depending on the metal oxidation states. In the known compounds, metal oxidation states are limited to either 3+ or mixed-valent 3+/4+. A multistep soft chemistry synthetic route for novel phases with M(2+/3+)O2 triangular layers is reported.

  8. Synthesis of Two Local Anesthetics from Toluene: An Organic Multistep Synthesis in a Project-Oriented Laboratory Course

    ERIC Educational Resources Information Center

    Demare, Patricia; Regla, Ignacio

    2012-01-01

    This article describes one of the projects in the advanced undergraduate organic chemistry laboratory course concerning the synthesis of two local anesthetic drugs, prilocaine and benzocaine, with a common three-step sequence starting from toluene. Students undertake, in a several-week independent project, the multistep synthesis of a…

  9. Self-Regulated Strategy Development Instruction for Teaching Multi-Step Equations to Middle School Students Struggling in Math

    ERIC Educational Resources Information Center

    Cuenca-Carlino, Yojanna; Freeman-Green, Shaqwana; Stephenson, Grant W.; Hauth, Clara

    2016-01-01

    Six middle school students identified as having a specific learning disability or at risk for mathematical difficulties were taught how to solve multi-step equations by using the self-regulated strategy development (SRSD) model of instruction. A multiple-probe-across-pairs design was used to evaluate instructional effects. Instruction was provided…

  10. A Multistep Organocatalysis Experiment for the Undergraduate Organic Laboratory: An Enantioselective Aldol Reaction Catalyzed by Methyl Prolinamide

    ERIC Educational Resources Information Center

    Wade, Edmir O.; Walsh, Kenneth E.

    2011-01-01

    In recent years, there has been an explosion of research concerning the area of organocatalysis. A multistep capstone laboratory project that combines traditional reactions frequently found in organic laboratory curriculums with this new field of research is described. In this experiment, the students synthesize a prolinamide-based organocatalyst…

  11. Synthesis of 10-Ethyl Flavin: A Multistep Synthesis Organic Chemistry Laboratory Experiment for Upper-Division Undergraduate Students

    ERIC Educational Resources Information Center

    Sichula, Vincent A.

    2015-01-01

    A multistep synthesis of 10-ethyl flavin was developed as an organic chemistry laboratory experiment for upper-division undergraduate students. Students synthesize 10-ethyl flavin as a bright yellow solid via a five-step sequence. The experiment introduces students to various hands-on experimental organic synthetic techniques, such as column…

  12. Synthesis of Frontalin, the Aggregation Pheromone of the Southern Pine Beetle: A Multistep Organic Synthesis for Undergraduate Students.

    ERIC Educational Resources Information Center

    Bartlett, Paul A.; And Others

    1984-01-01

    Background information and experimental procedures are provided for the multistep synthesis of frontalin. The experiment exposes students to a range of practical laboratory problems and important synthetic reactions and provides experiences in working on a medium-size, as well as a relatively small-size scale. (JN)

  13. Management Planning for Workplace Automation.

    ERIC Educational Resources Information Center

    McDole, Thomas L.

    Several factors must be considered when implementing office automation. Included among these are whether or not to automate at all, the effects of automation on employees, requirements imposed by automation on the physical environment, effects of automation on the total organization, and effects on clientele. The reasons behind the success or…

  14. Laboratory Automation and Middleware.

    PubMed

    Riben, Michael

    2015-06-01

    The practice of surgical pathology is under constant pressure to deliver the highest quality of service, reduce errors, increase throughput, and decrease turnaround time while at the same time dealing with an aging workforce, increasing financial constraints, and economic uncertainty. Although not able to implement total laboratory automation, great progress continues to be made in workstation automation in all areas of the pathology laboratory. This report highlights the benefits and challenges of pathology automation, reviews middleware and its use to facilitate automation, and reviews the progress so far in the anatomic pathology laboratory.

  15. Complacency and Automation Bias in the Use of Imperfect Automation.

    PubMed

    Wickens, Christopher D; Clegg, Benjamin A; Vieane, Alex Z; Sebok, Angelia L

    2015-08-01

    We examine the effects of two different kinds of decision-aiding automation errors on human-automation interaction (HAI), occurring at the first failure following repeated exposure to correctly functioning automation. The two errors are incorrect advice, triggering the automation bias, and missing advice, reflecting complacency. Contrasts between analogous automation errors in alerting systems, rather than decision aiding, have revealed that alerting false alarms are more problematic to HAI than alerting misses are. Prior research in decision aiding, although contrasting the two aiding errors (incorrect vs. missing), has confounded error expectancy. Participants performed an environmental process control simulation with and without decision aiding. For those with the aid, automation dependence was created through several trials of perfect aiding performance, and an unexpected automation error was then imposed in which automation was either gone (one group) or wrong (a second group). A control group received no automation support. The correct aid supported faster and more accurate diagnosis and lower workload. The aid failure degraded all three variables, but "automation wrong" had a much greater effect on accuracy, reflecting the automation bias, than did "automation gone," reflecting the impact of complacency. Some complacency was manifested for automation gone, by a longer latency and more modest reduction in accuracy. Automation wrong, creating the automation bias, appears to be a more problematic form of automation error than automation gone, reflecting complacency. Decision-aiding automation should indicate its lower degree of confidence in uncertain environments to avoid the automation bias. © 2015, Human Factors and Ergonomics Society.

  16. Automated DNA extraction from pollen in honey.

    PubMed

    Guertler, Patrick; Eicheldinger, Adelina; Muschler, Paul; Goerlich, Ottmar; Busch, Ulrich

    2014-04-15

    In recent years, honey has become subject of DNA analysis due to potential risks evoked by microorganisms, allergens or genetically modified organisms. However, so far, only a few DNA extraction procedures are available, mostly time-consuming and laborious. Therefore, we developed an automated DNA extraction method from pollen in honey based on a CTAB buffer-based DNA extraction using the Maxwell 16 instrument and the Maxwell 16 FFS Nucleic Acid Extraction System, Custom-Kit. We altered several components and extraction parameters and compared the optimised method with a manual CTAB buffer-based DNA isolation method. The automated DNA extraction was faster and resulted in higher DNA yield and sufficient DNA purity. Real-time PCR results obtained after automated DNA extraction are comparable to results after manual DNA extraction. No PCR inhibition was observed. The applicability of this method was further successfully confirmed by analysis of different routine honey samples. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Automating checks of plan check automation.

    PubMed

    Halabi, Tarek; Lu, Hsiao-Ming

    2014-07-08

    While a few physicists have designed new plan check automation solutions for their clinics, fewer, if any, managed to adapt existing solutions. As complex and varied as the systems they check, these programs must gain the full confidence of those who would run them on countless patient plans. The present automation effort, planCheck, therefore focuses on versatility and ease of implementation and verification. To demonstrate this, we apply planCheck to proton gantry, stereotactic proton gantry, stereotactic proton fixed beam (STAR), and IMRT treatments.

  18. Automation and Cataloging.

    ERIC Educational Resources Information Center

    Furuta, Kenneth; And Others

    1990-01-01

    These three articles address issues in library cataloging that are affected by automation: (1) the impact of automation and bibliographic utilities on professional catalogers; (2) the effect of the LASS microcomputer software on the cost of authority work in cataloging at the University of Arizona; and (3) online subject heading and classification…

  19. Order Division Automated System.

    ERIC Educational Resources Information Center

    Kniemeyer, Justin M.; And Others

    This publication was prepared by the Order Division Automation Project staff to fulfill the Library of Congress' requirement to document all automation efforts. The report was originally intended for internal use only and not for distribution outside the Library. It is now felt that the library community at-large may have an interest in the…

  20. More Benefits of Automation.

    ERIC Educational Resources Information Center

    Getz, Malcolm

    1988-01-01

    Describes a study that measured the benefits of an automated catalog and automated circulation system from the library user's point of view in terms of the value of time saved. Topics discussed include patterns of use, access time, availability of information, search behaviors, and the effectiveness of the measures used. (seven references)…

  1. Work and Programmable Automation.

    ERIC Educational Resources Information Center

    DeVore, Paul W.

    A new industrial era based on electronics and the microprocessor has arrived, an era that is being called intelligent automation. Intelligent automation, in the form of robots, replaces workers, and the new products, using microelectronic devices, require significantly less labor to produce than the goods they replace. The microprocessor thus…

  2. The Automated Office.

    ERIC Educational Resources Information Center

    Naclerio, Nick

    1979-01-01

    Clerical personnel may be able to climb career ladders as a result of office automation and expanded job opportunities in the word processing area. Suggests opportunities in an automated office system and lists books and periodicals on word processing for counselors and teachers. (MF)

  3. Planning for Office Automation.

    ERIC Educational Resources Information Center

    Sherron, Gene T.

    1982-01-01

    The steps taken toward office automation by the University of Maryland are described. Office automation is defined and some types of word processing systems are described. Policies developed in the writing of a campus plan are listed, followed by a section on procedures adopted to implement the plan. (Author/MLW)

  4. WANTED: Fully Automated Indexing.

    ERIC Educational Resources Information Center

    Purcell, Royal

    1991-01-01

    Discussion of indexing focuses on the possibilities of fully automated indexing. Topics discussed include controlled indexing languages such as subject heading lists and thesauri, free indexing languages, natural indexing languages, computer-aided indexing, expert systems, and the need for greater creativity to further advance automated indexing.…

  5. Advances in inspection automation

    NASA Astrophysics Data System (ADS)

    Weber, Walter H.; Mair, H. Douglas; Jansen, Dion; Lombardi, Luciano

    2013-01-01

    This new session at QNDE reflects the growing interest in inspection automation. Our paper describes a newly developed platform that makes the complex NDE automation possible without the need for software programmers. Inspection tasks that are tedious, error-prone or impossible for humans to perform can now be automated using a form of drag and drop visual scripting. Our work attempts to rectify the problem that NDE is not keeping pace with the rest of factory automation. Outside of NDE, robots routinely and autonomously machine parts, assemble components, weld structures and report progress to corporate databases. By contrast, components arriving in the NDT department typically require manual part handling, calibrations and analysis. The automation examples in this paper cover the development of robotic thickness gauging and the use of adaptive contour following on the NRU reactor inspection at Chalk River.

  6. Automation in Immunohematology

    PubMed Central

    Bajpai, Meenu; Kaur, Ravneet; Gupta, Ekta

    2012-01-01

    There have been rapid technological advances in blood banking in South Asian region over the past decade with an increasing emphasis on quality and safety of blood products. The conventional test tube technique has given way to newer techniques such as column agglutination technique, solid phase red cell adherence assay, and erythrocyte-magnetized technique. These new technologies are adaptable to automation and major manufacturers in this field have come up with semi and fully automated equipments for immunohematology tests in the blood bank. Automation improves the objectivity and reproducibility of tests. It reduces human errors in patient identification and transcription errors. Documentation and traceability of tests, reagents and processes and archiving of results is another major advantage of automation. Shifting from manual methods to automation is a major undertaking for any transfusion service to provide quality patient care with lesser turnaround time for their ever increasing workload. This article discusses the various issues involved in the process. PMID:22988378

  7. Development of Multistep and Degenerate Variational Integrators for Applications in Plasma Physics

    NASA Astrophysics Data System (ADS)

    Ellison, Charles Leland

    Geometric integrators yield high-fidelity numerical results by retaining conservation laws in the time advance. A particularly powerful class of geometric integrators is symplectic integrators, which are widely used in orbital mechanics and accelerator physics. An important application presently lacking symplectic integrators is the guiding center motion of magnetized particles represented by non-canonical coordinates. Because guiding center trajectories are foundational to many simulations of magnetically confined plasmas, geometric guiding center algorithms have high potential for impact. The motivation is compounded by the need to simulate long-pulse fusion devices, including ITER, and opportunities in high performance computing, including the use of petascale resources and beyond. This dissertation uses a systematic procedure for constructing geometric integrators --- known as variational integration --- to deliver new algorithms for guiding center trajectories and other plasma-relevant dynamical systems. These variational integrators are non-trivial because the Lagrangians of interest are degenerate - the Euler-Lagrange equations are first-order differential equations and the Legendre transform is not invertible. The first contribution of this dissertation is that variational integrators for degenerate Lagrangian systems are typically multistep methods. Multistep methods admit parasitic mode instabilities that can ruin the numerical results. These instabilities motivate the second major contribution: degenerate variational integrators. By replicating the degeneracy of the continuous system, degenerate variational integrators avoid parasitic mode instabilities. The new methods are therefore robust geometric integrators for degenerate Lagrangian systems. These developments in variational integration theory culminate in one-step degenerate variational integrators for non-canonical magnetic field line flow and guiding center dynamics. The guiding center integrator

  8. Development of Multistep and Degenerate Variational Integrators for Applications in Plasma Physics

    SciTech Connect

    Ellison, Charles Leland

    2016-04-01

    Geometric integrators yield high-fidelity numerical results by retaining conservation laws in the time advance. A particularly powerful class of geometric integrators is symplectic integrators, which are widely used in orbital mechanics and accelerator physics. An important application presently lacking symplectic integrators is the guiding center motion of magnetized particles represented by non-canonical coordinates. Because guiding center trajectories are foundational to many simulations of magnetically confined plasmas, geometric guiding center algorithms have high potential for impact. The motivation is compounded by the need to simulate long-pulse fusion devices, including ITER, and opportunities in high performance computing, including the use of petascale resources and beyond. This dissertation uses a systematic procedure for constructing geometric integrators - known as variational integration - to deliver new algorithms for guiding center trajectories and other plasma-relevant dynamical systems. These variational integrators are non-trivial because the Lagrangians of interest are degenerate - the Euler-Lagrange equations are first-order differential equations and the Legendre transform is not invertible. The first contribution of this dissertation is that variational integrators for degenerate Lagrangian systems are typically multistep methods. Multistep methods admit parasitic mode instabilities that can ruin the numerical results. These instabilities motivate the second major contribution: degenerate variational integrators. By replicating the degeneracy of the continuous system, degenerate variational integrators avoid parasitic mode instabilities. The new methods are therefore robust geometric integrators for degenerate Lagrangian systems. These developments in variational integration theory culminate in one-step degenerate variational integrators for non-canonical magnetic field line flow and guiding center dynamics. The guiding center integrator

  9. A multi-step transversal linearization (MTL) method in non-linear structural dynamics

    NASA Astrophysics Data System (ADS)

    Roy, D.; Kumar, Rajesh

    2005-10-01

    An implicit family of multi-step transversal linearization (MTL) methods is proposed for efficient and numerically stable integration of nonlinear oscillators of interest in structural dynamics. The presently developed method is a multi-step extension and further generalization of the locally transversal linearization (LTL) method proposed earlier by Roy (Proceedings of the Academy of the Royal Society (London) 457 (2001) 539-566), Roy and Ramachandra (Journal of Sound and Vibration 41 (2001a) 653-679, International Journal for Numerical Methods in Engineering 51 (2001b) 203-224) and Roy (International Journal of Numerical Methods in Engineering 61 (2004) 764). The MTL-based linearization is achieved through a non-unique replacement of the nonlinear part of the vector field by a conditionally linear interpolating expansion of known accuracy, whose coefficients contain the discretized state variables defined at a set of grid points. In the process, the nonlinear part of the vector field becomes a conditionally determinable equivalent forcing function. The MTL-based linearized differential equations thus become explicitly integrable. Based on the linearized solution, a set of algebraic, constraint equations are so formed that transversal intersections of the linearized and nonlinearized solution manifolds occur at the multiple grid points. The discretized state vectors are thus found as the zeros of the constraint equations. Simple error estimates for the displacement and velocity vectors are provided and, in particular, it is shown that the formal accuracy of the MTL methods as a function of the time step-size depends only on the error of replacement of the nonlinear part of the vector field. Presently, only two different polynomial-based interpolation schemes are employed for transversal linearization, viz. the Taylor-like interpolation and the Lagrangian interpolation. While the Taylor-like interpolation leads to numerical ill-conditioning as the order of

  10. Multistep nature of X-ray-induced neoplastic transformation in golden hamster embryo cells: expression of transformed phenotypes and stepwise changes in karyotypes

    SciTech Connect

    Suzuki, K.; Suzuki, F.; Watanabe, M.; Nikaido, O.

    1989-04-15

    We have examined the expression of transformed phenotypes and genetic changes associated with the expression of each transformed phenotype after X-ray irradiation. Unirradiated cells grown at a constant growth rate until 8 passages (population doubling number, 15) exhibited little morphological change and ceased to divide thereafter. X-irradiated cells escaped from senescence and showed morphological alteration and anchorage independence after a population doubling number of 20. The acquisition of tumorigenicity in nude mice was observed much later (35 population doublings after irradiation). From cytogenetic analysis, all anchorage-independent clones were consistently found to have trisomy of chromosome 7. Furthermore, cells derived from tumors contained three copies of chromosome 9q in addition to the trisomy of chromosome 7. We have not detected any augmented expression of v-Ha-ras- and v-myc-related oncogenes with RNA dot-blot analysis and could not find activation of any type of oncogenes by NIH3T3 transfection experiments. Our studies demonstrated that X-ray-induced neoplastic transformation is a multistep phenomenon and that the numerical change of specific chromosomes may play an important role in the expression of each transformed phenotype. The results suggest that different endogenous oncogenes, other than the ras gene family and myc oncogene, could be responsible for the progressive nature of neoplastic transformation.

  11. Systematic review automation technologies.

    PubMed

    Tsafnat, Guy; Glasziou, Paul; Choong, Miew Keen; Dunn, Adam; Galgani, Filippo; Coiera, Enrico

    2014-07-09

    Systematic reviews, a cornerstone of evidence-based medicine, are not produced quickly enough to support clinical practice. The cost of production, availability of the requisite expertise and timeliness are often quoted as major contributors for the delay. This detailed survey of the state of the art of information systems designed to support or automate individual tasks in the systematic review, and in particular systematic reviews of randomized controlled clinical trials, reveals trends that see the convergence of several parallel research projects.We surveyed literature describing informatics systems that support or automate the processes of systematic review or each of the tasks of the systematic review. Several projects focus on automating, simplifying and/or streamlining specific tasks of the systematic review. Some tasks are already fully automated while others are still largely manual. In this review, we describe each task and the effect that its automation would have on the entire systematic review process, summarize the existing information system support for each task, and highlight where further research is needed for realizing automation for the task. Integration of the systems that automate systematic review tasks may lead to a revised systematic review workflow. We envisage the optimized workflow will lead to system in which each systematic review is described as a computer program that automatically retrieves relevant trials, appraises them, extracts and synthesizes data, evaluates the risk of bias, performs meta-analysis calculations, and produces a report in real time.

  12. Systematic review automation technologies

    PubMed Central

    2014-01-01

    Systematic reviews, a cornerstone of evidence-based medicine, are not produced quickly enough to support clinical practice. The cost of production, availability of the requisite expertise and timeliness are often quoted as major contributors for the delay. This detailed survey of the state of the art of information systems designed to support or automate individual tasks in the systematic review, and in particular systematic reviews of randomized controlled clinical trials, reveals trends that see the convergence of several parallel research projects. We surveyed literature describing informatics systems that support or automate the processes of systematic review or each of the tasks of the systematic review. Several projects focus on automating, simplifying and/or streamlining specific tasks of the systematic review. Some tasks are already fully automated while others are still largely manual. In this review, we describe each task and the effect that its automation would have on the entire systematic review process, summarize the existing information system support for each task, and highlight where further research is needed for realizing automation for the task. Integration of the systems that automate systematic review tasks may lead to a revised systematic review workflow. We envisage the optimized workflow will lead to system in which each systematic review is described as a computer program that automatically retrieves relevant trials, appraises them, extracts and synthesizes data, evaluates the risk of bias, performs meta-analysis calculations, and produces a report in real time. PMID:25005128

  13. Carbon and hydrogen isotope fractionation of benzene and toluene during hydrophobic sorption in multistep batch experiments.

    PubMed

    Imfeld, G; Kopinke, F-D; Fischer, A; Richnow, H-H

    2014-07-01

    The application of compound-specific stable isotope analysis (CSIA) for evaluating degradation of organic pollutants in the field implies that other processes affecting pollutant concentration are minor with respect to isotope fractionation. Sorption is associated with minor isotope fractionation and pollutants may undergo successive sorption-desorption steps during their migration in aquifers. However, little is known about isotope fractionation of BTEX compounds after consecutive sorption steps. Here, we show that partitioning of benzene and toluene between water and organic sorbents (i.e. 1-octanol, dichloromethane, cyclohexane, hexanoic acid and Amberlite XAD-2) generally exhibits very small carbon and hydrogen isotope effects in multistep batch experiments. However, carbon and hydrogen isotope fractionation was observed for the benzene-octanol pair after several sorption steps (Δδ(13)C=1.6 ± 0.3‰ and Δδ(2)H=88 ± 3‰), yielding isotope fractionation factors of αC=1.0030 ± 0.0005 and αH=1.195 ± 0.026. Our results indicate that the cumulative effect of successive hydrophobic partitioning steps in an aquifer generally results in insignificant isotope fractionation for benzene and toluene. However, significant carbon and hydrogen isotope fractionation cannot be excluded for specific sorbate-sorbent pairs, such as sorbates with π-electrons and sorbents with OH-groups. Consequently, functional groups of sedimentary organic matter (SOM) may specifically interact with BTEX compounds migrating in an aquifer, thereby resulting in potentially relevant isotope fractionation.

  14. Spontaneous formation of the unlocked state of the ribosome is a multistep process.

    PubMed

    Munro, James B; Altman, Roger B; Tung, Chang-Shung; Cate, Jamie H D; Sanbonmatsu, Kevin Y; Blanchard, Scott C

    2010-01-12

    The mechanism of substrate translocation through the ribosome is central to the rapid and faithful translation of mRNA into proteins. The rate-limiting step in translocation is an unlocking process that includes the formation of an "unlocked" intermediate state, which requires the convergence of large-scale conformational events within the ribosome including tRNA hybrid states formation, closure of the ribosomal L1 stalk domain, and subunit ratcheting. Here, by imaging of the pretranslocation ribosome complex from multiple structural perspectives using two- and three-color single-molecule fluorescence resonance energy transfer, we observe that tRNA hybrid states formation and L1 stalk closure, events central to the unlocking mechanism, are not tightly coupled. These findings reveal that the unlocked state is achieved through a stochastic-multistep process, where the extent of conformational coupling depends on the nature of tRNA substrates. These data suggest that cellular mechanisms affecting the coupling of conformational processes on the ribosome may regulate the process of translation elongation.

  15. Spontaneous formation of the unlocked state of the ribosome is a multistep process

    PubMed Central

    Munro, James B.; Altman, Roger B.; Tung, Chang-Shung; Cate, Jamie H. D.; Sanbonmatsu, Kevin Y.; Blanchard, Scott C.

    2010-01-01

    The mechanism of substrate translocation through the ribosome is central to the rapid and faithful translation of mRNA into proteins. The rate-limiting step in translocation is an unlocking process that includes the formation of an “unlocked” intermediate state, which requires the convergence of large-scale conformational events within the ribosome including tRNA hybrid states formation, closure of the ribosomal L1 stalk domain, and subunit ratcheting. Here, by imaging of the pretranslocation ribosome complex from multiple structural perspectives using two- and three-color single-molecule fluorescence resonance energy transfer, we observe that tRNA hybrid states formation and L1 stalk closure, events central to the unlocking mechanism, are not tightly coupled. These findings reveal that the unlocked state is achieved through a stochastic-multistep process, where the extent of conformational coupling depends on the nature of tRNA substrates. These data suggest that cellular mechanisms affecting the coupling of conformational processes on the ribosome may regulate the process of translation elongation. PMID:20018653

  16. Investigation of the reactions of acrylamide during in vitro multistep enzymatic digestion of thermally processed foods.

    PubMed

    Hamzalıoğlu, Aytül; Gökmen, Vural

    2015-01-01

    This study investigated the fate of acrylamide in thermally processed foods after ingestion. An in vitro multistep enzymatic digestion system simulating gastric, duodenal and colon phases was used to understand the fate of acrylamide in bakery and fried potato products. Acrylamide levels gradually decreased through gastric, duodenal and colon phases during in vitro digestion of biscuits. At the end of digestion, acrylamide reduction was between 49.2% and 73.4% in biscuits. Binary model systems composed of acrylamide and amino acids were used to understand the mechanism of acrylamide reduction. High-resolution mass spectrometry analyses confirmed Michael addition of amino acids to acrylamide during digestion. In contrast to bakery products, acrylamide levels increased significantly during gastric digestion of fried potatoes. The Schiff base formed between reducing sugars and asparagine disappeared rapidly, whereas the acrylamide level increased during the gastric phase. This suggests that intermediates like the Schiff base that accumulate in potatoes during frying are potential precursors of acrylamide under gastric conditions.

  17. Multi-step process for concentrating magnetic particles in waste sludges

    DOEpatents

    Watson, J.L.

    1990-07-10

    This invention involves a multi-step, multi-force process for dewatering sludges which have high concentrations of magnetic particles, such as waste sludges generated during steelmaking. This series of processing steps involves (1) mixing a chemical flocculating agent with the sludge; (2) allowing the particles to aggregate under non-turbulent conditions; (3) subjecting the mixture to a magnetic field which will pull the magnetic aggregates in a selected direction, causing them to form a compacted sludge; (4) preferably, decanting the clarified liquid from the compacted sludge; and (5) using filtration to convert the compacted sludge into a cake having a very high solids content. Steps 2 and 3 should be performed simultaneously. This reduces the treatment time and increases the extent of flocculation and the effectiveness of the process. As partially formed aggregates with active flocculating groups are pulled through the mixture by the magnetic field, they will contact other particles and form larger aggregates. This process can increase the solids concentration of steelmaking sludges in an efficient and economic manner, thereby accomplishing either of two goals: (a) it can convert hazardous wastes into economic resources for recycling as furnace feed material, or (b) it can dramatically reduce the volume of waste material which must be disposed. 7 figs.

  18. Multi-step process for concentrating magnetic particles in waste sludges

    DOEpatents

    Watson, John L.

    1990-01-01

    This invention involves a multi-step, multi-force process for dewatering sludges which have high concentrations of magnetic particles, such as waste sludges generated during steelmaking. This series of processing steps involves (1) mixing a chemical flocculating agent with the sludge; (2) allowing the particles to aggregate under non-turbulent conditions; (3) subjecting the mixture to a magnetic field which will pull the magnetic aggregates in a selected direction, causing them to form a compacted sludge; (4) preferably, decanting the clarified liquid from the compacted sludge; and (5) using filtration to convert the compacted sludge into a cake having a very high solids content. Steps 2 and 3 should be performed simultaneously. This reduces the treatment time and increases the extent of flocculation and the effectiveness of the process. As partially formed aggregates with active flocculating groups are pulled through the mixture by the magnetic field, they will contact other particles and form larger aggregates. This process can increase the solids concentration of steelmaking sludges in an efficient and economic manner, thereby accomplishing either of two goals: (a) it can convert hazardous wastes into economic resources for recycling as furnace feed material, or (b) it can dramatically reduce the volume of waste material which must be disposed.

  19. Mid-infrared supercontinuum generation in chalcogenide multi-step index fibers with normal chromatic dispersion

    NASA Astrophysics Data System (ADS)

    Nagasaka, K.; Tong, Hoang Tuan; Liu, Lai; Matsumoto, Morio; Tezuka, Hiroshige; Suzuki, Takenobu; Ohishi, Yasutake

    2017-02-01

    We experimentally demonstrate mid-infrared supercontinuum (SC) generation in chalcogenide multi-step index fibers (MSIF) pumped by a femtosecond laser. The fabricated chalcogenide MSIF is composed of a high refractive index core (C1) in the center, which is enclosed by a lower refractive index core layer (C2) and an outer cladding. This fiber structure is advantageous to tailor the chromatic dispersion with higher freedom and to keep the effective mode area small at long wavelengths. The high refractive index core, low refractive index core, and the outer cladding materials are As2Se3, AsSe2 and As2S5, respectively. When the diameter of C1 and C2 are 7.8 and 30 μm, respectively, the zerodispersion wavelength (ZDW) of the fiber is 12.5 μm. The chromatic dispersion profile is near-zero and flattened within the range of +/-20 ps/km/nm in the wavelength range from 4 to 17 μm and a broad normal dispersion region is obtained in the wavelength range shorter than the ZDW. In practice, a 2.8 cm long fiber is pumped at 10 μm by using a femtosecond laser whose pulse width is 200 fs. The SC generation extending from 2 to 14 μm is obtained. Most of its spectrum is in the normal dispersion region of the fiber. These results are promising for the highly coherent mid-infrared SC generation.

  20. Link community detection by non-negative matrix factorization with multi-step similarities

    NASA Astrophysics Data System (ADS)

    Tang, Xianchao; Yang, Guoqing; Xu, Tao; Feng, Xia; Wang, Xiao; Li, Qiannan; Liu, Yanbei

    2016-11-01

    Uncovering community structures is a fundamental and important problem in analyzing the complex networks. While most of the methods focus on identifying node communities, recent works show the intuitions and advantages of detecting link communities in networks. In this paper, we propose a non-negative matrix factorization (NMF) based method to detect the link community structures. Traditional NMF-based methods mainly consider the adjacency matrix as the representation of network topology, while the adjacency matrix only shows the relationship between immediate neighbor nodes, which does not take the relationship between non-neighbor nodes into consideration. This may greatly reduce the information contained in the network topology, and thus leads to unsatisfactory results. Here, we address this by introducing multi-step similarities using the graph random walk approach so that the similarities between non-neighbor nodes can be captured. Meanwhile, in order to reduce impact caused by self-similarities (similarities between nodes themselves) and increase importance gained from similarities between other different nodes, we add a penalty term to our objective function. Then an efficient optimization scheme for the objective function is derived. Finally, we test the proposed method on both synthetic and real networks. Experimental results demonstrate the effectiveness of the proposed approach.

  1. Shutdown Dose Rate Analysis Using the Multi-Step CADIS Method

    SciTech Connect

    Ibrahim, Ahmad M.; Peplow, Douglas E.; Peterson, Joshua L.; Grove, Robert E.

    2015-01-01

    The Multi-Step Consistent Adjoint Driven Importance Sampling (MS-CADIS) hybrid Monte Carlo (MC)/deterministic radiation transport method was proposed to speed up the shutdown dose rate (SDDR) neutron MC calculation using an importance function that represents the neutron importance to the final SDDR. This work applied the MS-CADIS method to the ITER SDDR benchmark problem. The MS-CADIS method was also used to calculate the SDDR uncertainty resulting from uncertainties in the MC neutron calculation and to determine the degree of undersampling in SDDR calculations because of the limited ability of the MC method to tally detailed spatial and energy distributions. The analysis that used the ITER benchmark problem compared the efficiency of the MS-CADIS method to the traditional approach of using global MC variance reduction techniques for speeding up SDDR neutron MC calculation. Compared to the standard Forward-Weighted-CADIS (FW-CADIS) method, the MS-CADIS method increased the efficiency of the SDDR neutron MC calculation by 69%. The MS-CADIS method also increased the fraction of nonzero scoring mesh tally elements in the space-energy regions of high importance to the final SDDR.

  2. Complex network analysis of brain functional connectivity under a multi-step cognitive task

    NASA Astrophysics Data System (ADS)

    Cai, Shi-Min; Chen, Wei; Liu, Dong-Bai; Tang, Ming; Chen, Xun

    2017-01-01

    Functional brain network has been widely studied to understand the relationship between brain organization and behavior. In this paper, we aim to explore the functional connectivity of brain network under a multi-step cognitive task involving consecutive behaviors, and further understand the effect of behaviors on the brain organization. The functional brain networks are constructed based on a high spatial and temporal resolution fMRI dataset and analyzed via complex network based approach. We find that at voxel level the functional brain network shows robust small-worldness and scale-free characteristics, while its assortativity and rich-club organization are slightly restricted to the order of behaviors performed. More interestingly, the functional connectivity of brain network in activated ROIs strongly correlates with behaviors and is obviously restricted to the order of behaviors performed. These empirical results suggest that the brain organization has the generic properties of small-worldness and scale-free characteristics, and its diverse functional connectivity emerging from activated ROIs is strongly driven by these behavioral activities via the plasticity of brain.

  3. Design of a Multistep Phase Mask for High-Energy Terahertz Pulse Generation by Optical Rectification

    NASA Astrophysics Data System (ADS)

    Avetisyan, Y.; Makaryan, A.; Tadevosyan, V.; Tonouchi, M.

    2017-08-01

    A new scheme for generating high-energy terahertz (THz) pulses based on using a multistep phase mask (MSPM) is suggested and analyzed. The mask is placed on the entrance surface of the nonlinear optical (NLO) crystal eliminating the necessity of the imaging optics. In contrast to the contact grating method, introduction of large amounts of angular dispersion is avoided. The operation principle of the suggested scheme is based on the fact that the MSPM splits a single input beam into many smaller time-delayed "beamlets," which together form a discretely tilted-front laser pulse in NLO crystal. The analysis of THz-pulse generation in ZnTe and lithium niobate (LN) crystals shows that application of ZnTe crystal is more preferable, especially when long-wavelength pump sources are used. The dimensions of the mask's steps required for high-energy THz-pulse generation in ZnTe and LN crystals are calculated. The optimal number of steps is estimated, taking into account individual beamlet's spatial broadening and problems related to the mask fabrication. The proposed method is a promising way to develop high-energy, monolithic, and alignment-free THz-pulse sources.

  4. Stochastic diffusion model of multistep activation in a voltage-dependent K channel

    NASA Astrophysics Data System (ADS)

    Vaccaro, S. R.

    2010-04-01

    The energy barrier to the activated state for the S4 voltage sensor of a K channel is dependent on the electrostatic force between positively charged S4 residues and negatively charged groups on neighboring segments, the potential difference across the membrane, and the dielectric boundary force on the charged residues near the interface between the solvent and the low dielectric region of the membrane gating pore. The variation of the potential function with transverse displacement and rotation of the S4 sensor across the membrane may be derived from a solution of Poisson's equation for the electrostatic potential. By approximating the energy of an S4 sensor along a path between stationary states by a piecewise linear function of the transverse displacement, the dynamics of slow activation, in the millisecond range, may be described by the lowest frequency component of an analytical solution of interacting diffusion equations of Fokker-Planck type for resting and barrier regions. The solution of the Smoluchowski equations for an S4 sensor in an energy landscape with several barriers is in accord with an empirical master equation for multistep activation in a voltage-dependent K channel.

  5. Michaelis-Menten kinetics in shear flow: Similarity solutions for multi-step reactions.

    PubMed

    Ristenpart, W D; Stone, H A

    2012-03-01

    Models for chemical reaction kinetics typically assume well-mixed conditions, in which chemical compositions change in time but are uniform in space. In contrast, many biological and microfluidic systems of interest involve non-uniform flows where gradients in flow velocity dynamically alter the effective reaction volume. Here, we present a theoretical framework for characterizing multi-step reactions that occur when an enzyme or enzymatic substrate is released from a flat solid surface into a linear shear flow. Similarity solutions are developed for situations where the reactions are sufficiently slow compared to a convective time scale, allowing a regular perturbation approach to be employed. For the specific case of Michaelis-Menten reactions, we establish that the transversally averaged concentration of product scales with the distance x downstream as x(5/3). We generalize the analysis to n-step reactions, and we discuss the implications for designing new microfluidic kinetic assays to probe the effect of flow on biochemical processes.

  6. Multistep Reaction Based De Novo Drug Design: Generating Synthetically Feasible Design Ideas.

    PubMed

    Masek, Brian B; Baker, David S; Dorfman, Roman J; DuBrucq, Karen; Francis, Victoria C; Nagy, Stephan; Richey, Bree L; Soltanshahi, Farhad

    2016-04-25

    We describe a "multistep reaction driven" evolutionary algorithm approach to de novo molecular design. Structures generated by the approach include a proposed synthesis path intended to aid the chemist in assessing the synthetic feasibility of the ideas that are generated. The methodology is independent of how the design ideas are scored, allowing multicriteria drug design to address multiple issues including activity at one or more pharmacological targets, selectivity, physical and ADME properties, and off target liabilities; the methods are compatible with common computer-aided drug discovery "scoring" methodologies such as 2D- and 3D-ligand similarity, docking, desirability functions based on physiochemical properties, and/or predictions from 2D/3D QSAR or machine learning models and combinations thereof to be used to guide design. We have performed experiments to assess the extent to which known drug space can be covered by our approach. Using a library of 88 generic reactions and a database of ∼20 000 reactants, we find that our methods can identify "close" analogs for ∼50% of the known small molecule drugs with molecular weight less than 300. To assess the quality of the in silico generated synthetic pathways, synthesis chemists were asked to rate the viability of synthesis pathways: both "real" and in silico generated. In silico reaction schemes generated by our methods were rated as very plausible with scores similar to known literature synthesis schemes.

  7. Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2).

    PubMed Central

    Bała, P; Grochowski, P; Nowiński, K; Lesyng, B; McCammon, J A

    2000-01-01

    A quantum-classical molecular dynamics model (QCMD), applying explicit integration of the time-dependent Schrödinger equation (QD) and Newtonian equations of motion (MD), is presented. The model is capable of describing quantum dynamical processes in complex biomolecular systems. It has been applied in simulations of a multistep catalytic process carried out by phospholipase A(2) in its active site. The process includes quantum-dynamical proton transfer from a water molecule to histidine localized in the active site, followed by a nucleophilic attack of the resulting OH(-) group on a carbonyl carbon atom of a phospholipid substrate, leading to cleavage of an adjacent ester bond. The process has been simulated using a parallel version of the QCMD code. The potential energy function for the active site is computed using an approximate valence bond (AVB) method. The dynamics of the key proton is described either by QD or classical MD. The coupling between the quantum proton and the classical atoms is accomplished via Hellmann-Feynman forces, as well as the time dependence of the potential energy function in the Schrödinger equation (QCMD/AVB model). Analysis of the simulation results with an Advanced Visualization System revealed a correlated rather than a stepwise picture of the enzymatic process. It is shown that an sp(2)--> sp(3) configurational change at the substrate carbonyl carbon is mostly responsible for triggering the activation process. PMID:10968989

  8. Shutdown Dose Rate Analysis Using the Multi-Step CADIS Method

    DOE PAGES

    Ibrahim, Ahmad M.; Peplow, Douglas E.; Peterson, Joshua L.; ...

    2015-01-01

    The Multi-Step Consistent Adjoint Driven Importance Sampling (MS-CADIS) hybrid Monte Carlo (MC)/deterministic radiation transport method was proposed to speed up the shutdown dose rate (SDDR) neutron MC calculation using an importance function that represents the neutron importance to the final SDDR. This work applied the MS-CADIS method to the ITER SDDR benchmark problem. The MS-CADIS method was also used to calculate the SDDR uncertainty resulting from uncertainties in the MC neutron calculation and to determine the degree of undersampling in SDDR calculations because of the limited ability of the MC method to tally detailed spatial and energy distributions. The analysismore » that used the ITER benchmark problem compared the efficiency of the MS-CADIS method to the traditional approach of using global MC variance reduction techniques for speeding up SDDR neutron MC calculation. Compared to the standard Forward-Weighted-CADIS (FW-CADIS) method, the MS-CADIS method increased the efficiency of the SDDR neutron MC calculation by 69%. The MS-CADIS method also increased the fraction of nonzero scoring mesh tally elements in the space-energy regions of high importance to the final SDDR.« less

  9. Exact free vibration of multi-step Timoshenko beam system with several attachments

    NASA Astrophysics Data System (ADS)

    Farghaly, S. H.; El-Sayed, T. A.

    2016-05-01

    This paper deals with the analysis of the natural frequencies, mode shapes of an axially loaded multi-step Timoshenko beam combined system carrying several attachments. The influence of system design and the proposed sub-system non-dimensional parameters on the combined system characteristics are the major part of this investigation. The effect of material properties, rotary inertia and shear deformation of the beam system for each span are included. The end masses are elastically supported against rotation and translation at an offset point from the point of attachment. A sub-system having two degrees of freedom is located at the beam ends and at any of the intermediate stations and acts as a support and/or a suspension. The boundary conditions of the ordinary differential equation governing the lateral deflections and slope due to bending of the beam system including the shear force term, due to the sub-system, have been formulated. Exact global coefficient matrices for the combined modal frequencies, the modal shape and for the discrete sub-system have been derived. Based on these formulae, detailed parametric studies of the combined system are carried out. The applied mathematical model is valid for wide range of applications especially in mechanical, naval and structural engineering fields.

  10. Stochastic online appointment scheduling of multi-step sequential procedures in nuclear medicine.

    PubMed

    Pérez, Eduardo; Ntaimo, Lewis; Malavé, César O; Bailey, Carla; McCormack, Peter

    2013-12-01

    The increased demand for medical diagnosis procedures has been recognized as one of the contributors to the rise of health care costs in the U.S. in the last few years. Nuclear medicine is a subspecialty of radiology that uses advanced technology and radiopharmaceuticals for the diagnosis and treatment of medical conditions. Procedures in nuclear medicine require the use of radiopharmaceuticals, are multi-step, and have to be performed under strict time window constraints. These characteristics make the scheduling of patients and resources in nuclear medicine challenging. In this work, we derive a stochastic online scheduling algorithm for patient and resource scheduling in nuclear medicine departments which take into account the time constraints imposed by the decay of the radiopharmaceuticals and the stochastic nature of the system when scheduling patients. We report on a computational study of the new methodology applied to a real clinic. We use both patient and clinic performance measures in our study. The results show that the new method schedules about 600 more patients per year on average than a scheduling policy that was used in practice by improving the way limited resources are managed at the clinic. The new methodology finds the best start time and resources to be used for each appointment. Furthermore, the new method decreases patient waiting time for an appointment by about two days on average.

  11. Potential Lung Nodules Identification for Characterization by Variable Multistep Threshold and Shape Indices from CT Images

    PubMed Central

    Iqbal, Saleem; Iqbal, Khalid; Shaukat, Arslan; Khanum, Aasia

    2014-01-01

    Computed tomography (CT) is an important imaging modality. Physicians, surgeons, and oncologists prefer CT scan for diagnosis of lung cancer. However, some nodules are missed in CT scan. Computer aided diagnosis methods are useful for radiologists for detection of these nodules and early diagnosis of lung cancer. Early detection of malignant nodule is helpful for treatment. Computer aided diagnosis of lung cancer involves lung segmentation, potential nodules identification, features extraction from the potential nodules, and classification of the nodules. In this paper, we are presenting an automatic method for detection and segmentation of lung nodules from CT scan for subsequent features extraction and classification. Contribution of the work is the detection and segmentation of small sized nodules, low and high contrast nodules, nodules attached with vasculature, nodules attached to pleura membrane, and nodules in close vicinity of the diaphragm and lung wall in one-go. The particular techniques of the method are multistep threshold for the nodule detection and shape index threshold for false positive reduction. We used 60 CT scans of “Lung Image Database Consortium-Image Database Resource Initiative” taken by GE medical systems LightSpeed16 scanner as dataset and correctly detected 92% nodules. The results are reproducible. PMID:25506388

  12. Multistep damage evolution process in cubic zirconia irradiated with MeV ions

    SciTech Connect

    Moll, S.; Thome, L.; Debelle, A.; Garrido, F.; Vincent, L.; Sattonnay, G.

    2009-10-01

    This work reports the study, via the combination of Rutherford backscattering spectrometry and channeling, x-ray diffraction, and transmission electron microscopy experiments, of the damage formation in cubic yttria-stabilized zirconia single crystals irradiated with medium-energy (4 MeV) heavy (Au) ions. The damage buildup, which is accounted for in the framework of the multistep damage accumulation model, occurs in three steps. The first step at low fluences (up to 10{sup 15} cm{sup -2}), characterized by a regular increase in both the damage yield and the elastic strain, is related to the formation of small defect clusters. The second step in the intermediate fluence range (from 10{sup 15} to 5x10{sup 15} cm{sup -2}) leads to a sharp increase in the damage yield and to a large drop of the strain due to the formation of dislocation loops which collapse into a network of tangled dislocations. The third step at high fluences (above 5x10{sup 15} cm{sup -2}) exhibits a surprising decrease in the damage yield, which may be attributed to the reorganization of the dislocation network that leads to the formation of weakly damaged regions with a size of the order of 100 nm.

  13. Multistep continuous-flow synthesis of (R)- and (S)-rolipram using heterogeneous catalysts

    NASA Astrophysics Data System (ADS)

    Tsubogo, Tetsu; Oyamada, Hidekazu; Kobayashi, Shū

    2015-04-01

    Chemical manufacturing is conducted using either batch systems or continuous-flow systems. Flow systems have several advantages over batch systems, particularly in terms of productivity, heat and mixing efficiency, safety, and reproducibility. However, for over half a century, pharmaceutical manufacturing has used batch systems because the synthesis of complex molecules such as drugs has been difficult to achieve with continuous-flow systems. Here we describe the continuous-flow synthesis of drugs using only columns packed with heterogeneous catalysts. Commercially available starting materials were successively passed through four columns containing achiral and chiral heterogeneous catalysts to produce (R)-rolipram, an anti-inflammatory drug and one of the family of γ-aminobutyric acid (GABA) derivatives. In addition, simply by replacing a column packed with a chiral heterogeneous catalyst with another column packed with the opposing enantiomer, we obtained antipole (S)-rolipram. Similarly, we also synthesized (R)-phenibut, another drug belonging to the GABA family. These flow systems are simple and stable with no leaching of metal catalysts. Our results demonstrate that multistep (eight steps in this case) chemical transformations for drug synthesis can proceed smoothly under flow conditions using only heterogeneous catalysts, without the isolation of any intermediates and without the separation of any catalysts, co-products, by-products, and excess reagents. We anticipate that such syntheses will be useful in pharmaceutical manufacturing.

  14. Michaelis-Menten kinetics in shear flow: Similarity solutions for multi-step reactions

    PubMed Central

    Ristenpart, W. D.; Stone, H. A.

    2012-01-01

    Models for chemical reaction kinetics typically assume well-mixed conditions, in which chemical compositions change in time but are uniform in space. In contrast, many biological and microfluidic systems of interest involve non-uniform flows where gradients in flow velocity dynamically alter the effective reaction volume. Here, we present a theoretical framework for characterizing multi-step reactions that occur when an enzyme or enzymatic substrate is released from a flat solid surface into a linear shear flow. Similarity solutions are developed for situations where the reactions are sufficiently slow compared to a convective time scale, allowing a regular perturbation approach to be employed. For the specific case of Michaelis-Menten reactions, we establish that the transversally averaged concentration of product scales with the distance x downstream as x5/3. We generalize the analysis to n-step reactions, and we discuss the implications for designing new microfluidic kinetic assays to probe the effect of flow on biochemical processes. PMID:22662093

  15. Potential lung nodules identification for characterization by variable multistep threshold and shape indices from CT images.

    PubMed

    Iqbal, Saleem; Iqbal, Khalid; Arif, Fahim; Shaukat, Arslan; Khanum, Aasia

    2014-01-01

    Computed tomography (CT) is an important imaging modality. Physicians, surgeons, and oncologists prefer CT scan for diagnosis of lung cancer. However, some nodules are missed in CT scan. Computer aided diagnosis methods are useful for radiologists for detection of these nodules and early diagnosis of lung cancer. Early detection of malignant nodule is helpful for treatment. Computer aided diagnosis of lung cancer involves lung segmentation, potential nodules identification, features extraction from the potential nodules, and classification of the nodules. In this paper, we are presenting an automatic method for detection and segmentation of lung nodules from CT scan for subsequent features extraction and classification. Contribution of the work is the detection and segmentation of small sized nodules, low and high contrast nodules, nodules attached with vasculature, nodules attached to pleura membrane, and nodules in close vicinity of the diaphragm and lung wall in one-go. The particular techniques of the method are multistep threshold for the nodule detection and shape index threshold for false positive reduction. We used 60 CT scans of "Lung Image Database Consortium-Image Database Resource Initiative" taken by GE medical systems LightSpeed16 scanner as dataset and correctly detected 92% nodules. The results are reproducible.

  16. Multi-step sequential batch two-phase anaerobic composting of food waste.

    PubMed

    Shin, H S; Han, S K; Song, Y C; Lee, C Y

    2001-03-01

    This study was conducted to evaluate the newly devised process, called MUlti-step Sequential batch Two-phase Anaerobic Composting (MUSTAC). The MUSTAC process consisted of several leaching beds for hydrolysis, acidification and post-treatment, and a UASB reactor for methane recovery. This process to treat food waste was developed with a high-rate anaerobic composting technique based on the rate-limiting step approach. Rumen microorganisms were inoculated to improve the low efficiency of acidogenic fermentation. Both two-phase anaerobic digestion and sequential batch operation were used to control environmental constraints in anaerobic degradation. The MUSTAC process demonstrated excellent performance as it resulted in a large reduction in volatile solids (VS) (84.7%) and high methane conversion efficiency (84.4%) at high organic loading rates (10.8 kg VS m(-3) d(-1)) in a short SRT (10 days). Methane yield was 0.27 m3 kg(-1) VS, while methane gas production rate was 2.27 m3 m(-3) d(-1). The output from the post-treatment could be used as a soil amendment, which was produced at the same acidogenic fermenter without troublesome moving. The main advantages of the MUSTAC process were simple operation and high efficiency. The MUSTAC process proved stable, reliable and effective in resource recovery as well as waste stabilization.

  17. Multistep production of bioengineered skin substitutes: sequential modulation of culture conditions.

    PubMed

    Auger, F A; Pouliot, R; Tremblay, N; Guignard, R; Noël, P; Juhasz, J; Germain, L; Goulet, F

    2000-02-01

    Many studies are being conducted to define the role of growth factors in cutaneous physiology in order to add cytokines in a timely fashion for optimal tissue engineering of skin. This study is aimed at developing a multistep approach for the production of bioengineered skin substitutes, taking into account the effects of various growth factors according to the culture time. The use of a serum-supplemented medium throughout the whole culture period of skin substitutes was compared to the sequential use of specific additives at defined culture steps. Histological analysis revealed that serum was necessary for keratinocyte proliferation and migration on dermal substitutes during the first 2 d after their seeding. However, the serum-free medium presented some advantages when supplemented with different additives at specific culture steps. Interestingly, ascorbic acid added to the dermal substitutes before and after keratinocyte seeding maintained their cuboidal morphology in the basal epidermal layer. In the absence of serum, collagen matrix degradation slowed down, and a better multilayered epidermal organization was obtained, notably with retinoic acid. Stratum corneum formation was also enhanced by fatty acids. Thus, sequential addition of exogenous factors to the medium used to produce skin substitutes can improve their structural features and functional properties in vitro.

  18. Constrained Broyden Dimer Method with Bias Potential for Exploring Potential Energy Surface of Multistep Reaction Process.

    PubMed

    Shang, Cheng; Liu, Zhi-Pan

    2012-07-10

    To predict the chemical activity of new matter is an ultimate goal in chemistry. The identification of reaction pathways using modern quantum mechanics calculations, however, often requires a high demand in computational power and good chemical intuition on the reaction. Here, a new reaction path searching method is developed by combining our recently developed transition state (TS) location method, namely, the constrained Broyden dimer method, with a basin-filling method via bias potentials, which allows the system to walk out from the energy traps at a given reaction direction. In the new method, the reaction path searching starts from an initial state without the need for preguessing the TS-like or final state structure and can proceed iteratively to the final state by locating all related TSs and intermediates. In each elementary reaction step, a reaction direction, such as a bond breaking, needs to be specified, the information of which is refined and preserved as a normal mode through biased dimer rotation. The method is tested successfully on the Baker reaction system (50 elementary reactions) with good efficiency and stability and is also applied to the potential energy surface exploration of multistep reaction processes in the gas phase and on the surface. The new method can be applied for the computational screening of new catalytic materials with a minimum requirement of chemical intuition.

  19. Multistep continuous-flow synthesis of (R)- and (S)-rolipram using heterogeneous catalysts.

    PubMed

    Tsubogo, Tetsu; Oyamada, Hidekazu; Kobayashi, Shū

    2015-04-16

    Chemical manufacturing is conducted using either batch systems or continuous-flow systems. Flow systems have several advantages over batch systems, particularly in terms of productivity, heat and mixing efficiency, safety, and reproducibility. However, for over half a century, pharmaceutical manufacturing has used batch systems because the synthesis of complex molecules such as drugs has been difficult to achieve with continuous-flow systems. Here we describe the continuous-flow synthesis of drugs using only columns packed with heterogeneous catalysts. Commercially available starting materials were successively passed through four columns containing achiral and chiral heterogeneous catalysts to produce (R)-rolipram, an anti-inflammatory drug and one of the family of γ-aminobutyric acid (GABA) derivatives. In addition, simply by replacing a column packed with a chiral heterogeneous catalyst with another column packed with the opposing enantiomer, we obtained antipole (S)-rolipram. Similarly, we also synthesized (R)-phenibut, another drug belonging to the GABA family. These flow systems are simple and stable with no leaching of metal catalysts. Our results demonstrate that multistep (eight steps in this case) chemical transformations for drug synthesis can proceed smoothly under flow conditions using only heterogeneous catalysts, without the isolation of any intermediates and without the separation of any catalysts, co-products, by-products, and excess reagents. We anticipate that such syntheses will be useful in pharmaceutical manufacturing.

  20. Monte Carlo simulation of electrodeposition of copper: a multistep free energy calculation.

    PubMed

    Harinipriya, S; Subramanian, Venkat R

    2008-04-03

    Electrodeposition of copper (Cu) involves length scales of a micrometer or even less. Several theoretical techniques such as continuum Monte Carlo, kinetic Monte Carlo (KMC), and molecular dynamics have been used for simulating this problem. However the multiphenomena characteristics of the problem pose a challenge for an efficient simulation algorithm. Traditional KMC methods are slow, especially when modeling surface diffusion with large number of particles and frequent particle jumps. Parameter estimation involving thousands of KMC runs is very time-consuming. Thus a less time-consuming and novel multistep continuum Monte Carlo simulation is carried out to evaluate the step wise free energy change in the process of electrochemical copper deposition. The procedure involves separate Monte Carlo codes employing different random number criterion (using hydrated radii, bare radii, hydration number of the species, redox potentials, etc.) to obtain the number of species (CuCl(2) or CuSO(4) or Cu as the case may be) and in turn the free energy. The effect of concentration of electrolyte, influence of electric field and presence of chloride ions on the free energy change for the processes is studied. The rate determining step for the process of electrodeposition of copper from CuCl(2) and CuSO(4) is also determined.

  1. EpiJen: a server for multistep T cell epitope prediction

    PubMed Central

    Doytchinova, Irini A; Guan, Pingping; Flower, Darren R

    2006-01-01

    Background The main processing pathway for MHC class I ligands involves degradation of proteins by the proteasome, followed by transport of products by the transporter associated with antigen processing (TAP) to the endoplasmic reticulum (ER), where peptides are bound by MHC class I molecules, and then presented on the cell surface by MHCs. The whole process is modeled here using an integrated approach, which we call EpiJen. EpiJen is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes. EpiJen is available free online. Results To identify epitopes, a source protein is passed through four steps: proteasome cleavage, TAP transport, MHC binding and epitope selection. At each stage, different proportions of non-epitopes are eliminated. The final set of peptides represents no more than 5% of the whole protein sequence and will contain 85% of the true epitopes, as indicated by external validation. Compared to other integrated methods (NetCTL, WAPP and SMM), EpiJen performs best, predicting 61 of the 99 HIV epitopes used in this study. Conclusion EpiJen is a reliable multi-step algorithm for T cell epitope prediction, which belongs to the next generation of in silico T cell epitope identification methods. These methods aim to reduce subsequent experimental work by improving the success rate of epitope prediction. PMID:16533401

  2. Transformation of quiescent adult oligodendrocyte precursor cells into malignant glioma through a multistep reactivation process.

    PubMed

    Galvao, Rui Pedro; Kasina, Anita; McNeill, Robert S; Harbin, Jordan E; Foreman, Oded; Verhaak, Roel G W; Nishiyama, Akiko; Miller, C Ryan; Zong, Hui

    2014-10-07

    How malignant gliomas arise in a mature brain remains a mystery, hindering the development of preventive and therapeutic interventions. We previously showed that oligodendrocyte precursor cells (OPCs) can be transformed into glioma when mutations are introduced perinatally. However, adult OPCs rarely proliferate compared with their perinatal counterparts. Whether these relatively quiescent cells have the potential to transform is unknown, which is a critical question considering the late onset of human glioma. Additionally, the premalignant events taking place between initial mutation and a fully developed tumor mass are particularly poorly understood in glioma. Here we used a temporally controllable Cre transgene to delete p53 and NF1 specifically in adult OPCs and demonstrated that these cells consistently give rise to malignant gliomas. To investigate the transforming process of quiescent adult OPCs, we then tracked these cells throughout the premalignant phase, which revealed a dynamic multistep transformation, starting with rapid but transient hyperproliferative reactivation, followed by a long period of dormancy, and then final malignant transformation. Using pharmacological approaches, we discovered that mammalian target of rapamycin signaling is critical for both the initial OPC reactivation step and late-stage tumor cell proliferation and thus might be a potential target for both glioma prevention and treatment. In summary, our results firmly establish the transforming potential of adult OPCs and reveal an actionable multiphasic reactivation process that turns slowly dividing OPCs into malignant gliomas.

  3. Multistep Aggregation Pathway of Human Interleukin-1 Receptor Antagonist: Kinetic, Structural, and Morphological Characterization

    PubMed Central

    Krishnan, Sampathkumar; Raibekas, Andrei A.

    2009-01-01

    Abstract The complex, multistep aggregation kinetic and structural behavior of human recombinant interleukin-1 receptor antagonist (IL-1ra) was revealed and characterized by spectral probes and techniques. At a certain range of protein concentration (12–27 mg/mL) and temperature (44–48°C), two sequential aggregation kinetic transitions emerge, where the second transition is preceded by a lag phase and is associated with the main portion of the aggregated protein. Each kinetic transition is linked to a different type of aggregate population, referred to as type I and type II. The aggregate populations, isolated at a series of time points and analyzed by Fourier-transform infrared spectroscopy, show consecutive protein structural changes, from intramolecular (type I) to intermolecular (type II) β-sheet formation. The early type I protein spectral change resembles that seen for IL-1ra in the crystalline state. Moreover, Fourier-transform infrared data demonstrate that type I protein assembly alone can undergo a structural rearrangement and, consequently, convert to the type II aggregate. The aggregated protein structural changes are accompanied by the aggregate morphological changes, leading to a well-defined population of interacting spheres, as detected by scanning electron microscopy. A nucleation-driven IL-1ra aggregation pathway is proposed, and assumes two major activation energy barriers, where the second barrier is associated with the type I → type II aggregate structural rearrangement that, in turn, serves as a pseudonucleus triggering the second kinetic event. PMID:19134476

  4. Optimization of a Multi-Step Procedure for Isolation of Chicken Bone Collagen

    PubMed Central

    2015-01-01

    Chicken bone is not adequately utilized despite its high nutritional value and protein content. Although not a common raw material, chicken bone can be used in many different ways besides manufacturing of collagen products. In this study, a multi-step procedure was optimized to isolate chicken bone collagen for higher yield and quality for manufacture of collagen products. The chemical composition of chicken bone was 2.9% nitrogen corresponding to about 15.6% protein, 9.5% fat, 14.7% mineral and 57.5% moisture. The lowest amount of protein loss was aimed along with the separation of the highest amount of visible impurities, non-collagen proteins, minerals and fats. Treatments under optimum conditions removed 57.1% of fats and 87.5% of minerals with respect to their initial concentrations. Meanwhile, 18.6% of protein and 14.9% of hydroxyproline were lost, suggesting that a selective separation of non-collagen components and isolation of collagen were achieved. A significant part of impurities were selectively removed and over 80% of the original collagen was preserved during the treatments. PMID:26761863

  5. Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes.

    PubMed

    Xu, Jiajiong; Tang, Wei; Ma, Jun; Wang, Hong

    2017-04-11

    Drinking water treatment processes remove undesirable chemicals and microorganisms from source water, which is vital to public health protection. The purpose of this study was to investigate the effects of treatment processes and configuration on the microbiome by comparing microbial community shifts in two series of different treatment processes operated in parallel within a full-scale drinking water treatment plant (DWTP) in Southeast China. Illumina sequencing of 16S rRNA genes of water samples demonstrated little effect of coagulation/sedimentation and pre-oxidation steps on bacterial communities, in contrast to dramatic and concurrent microbial community shifts during ozonation, granular activated carbon treatment, sand filtration, and disinfection for both series. A large number of unique operational taxonomic units (OTUs) at these four treatment steps further illustrated their strong shaping power towards the drinking water microbial communities. Interestingly, multidimensional scaling analysis revealed tight clustering of biofilm samples collected from different treatment steps, with Nitrospira, the nitrite-oxidizing bacteria, noted at higher relative abundances in biofilm compared to water samples. Overall, this study provides a snapshot of step-to-step microbial evolvement in multi-step drinking water treatment systems, and the results provide insight to control and manipulation of the drinking water microbiome via optimization of DWTP design and operation.

  6. Surface Modified Particles By Multi-Step Michael-Type Addition And Process For The Preparation Thereof

    DOEpatents

    Cook, Ronald Lee; Elliott, Brian John; Luebben, Silvia DeVito; Myers, Andrew William; Smith, Bryan Matthew

    2005-05-03

    A new class of surface modified particles and a multi-step Michael-type addition surface modification process for the preparation of the same is provided. The multi-step Michael-type addition surface modification process involves two or more reactions to compatibilize particles with various host systems and/or to provide the particles with particular chemical reactivities. The initial step comprises the attachment of a small organic compound to the surface of the inorganic particle. The subsequent steps attach additional compounds to the previously attached organic compounds through reactive organic linking groups. Specifically, these reactive groups are activated carbon—carbon pi bonds and carbon and non-carbon nucleophiles that react via Michael or Michael-type additions.

  7. Comparison of surface roughness of nanofilled and nanohybrid composite resins after polishing with a multi-step technique

    NASA Astrophysics Data System (ADS)

    Itanto, B. S. H.; Usman, M.; Margono, A.

    2017-08-01

    To compare the surface roughness of nanofilled and nanohybrid composite resins after polishing using a multi-step technique. 40 composite resin specimens were divided into two groups (20 nanofilled specimens using Filtek Z350 XT [group A] and 20 nanohybrid specimens using Filtek Z250 XT [group B]), prepared, and then polished. After immersion in artificial saliva for 24 hours, the surface roughness was measured with a surface roughness tester. The mean surface roughness results along with the standard deviation of group A were 0.0967 μm ± 0.0174, while the results of group B were 0.1217 μm ± 0.0244. Statistically (with p = 0.05), there were significant differences between each group. The surface roughness of a nanofilled composite resin after polishing with a multi-step technique is better than that of a nanohybrid composite resin.

  8. Method to Improve Indium Bump Bonding via Indium Oxide Removal Using a Multi-Step Plasma Process

    NASA Technical Reports Server (NTRS)

    Greer, H. Frank (Inventor); Jones, Todd J. (Inventor); Vasquez, Richard P. (Inventor); Hoenk, Michael E. (Inventor); Dickie, Matthew R. (Inventor); Nikzad, Shouleh (Inventor)

    2012-01-01

    A process for removing indium oxide from indium bumps in a flip-chip structure to reduce contact resistance, by a multi-step plasma treatment. A first plasma treatment of the indium bumps with an argon, methane and hydrogen plasma reduces indium oxide, and a second plasma treatment with an argon and hydrogen plasma removes residual organics. The multi-step plasma process for removing indium oxide from the indium bumps is more effective in reducing the oxide, and yet does not require the use of halogens, does not change the bump morphology, does not attack the bond pad material or under-bump metallization layers, and creates no new mechanisms for open circuits.

  9. The automation of clinical trial serious adverse event reporting workflow

    PubMed Central

    London, Jack W; Smalley, Karl J; Conner, Kyle; Smith, J Bruce

    2011-01-01

    Background The reporting of serious adverse events (SAEs) is a requirement when conducting a clinical trial involving human subjects, necessary for the protection of the participants. The reporting process is a multi-step procedure, involving a number of individuals from initiation to final review, and must be completed in a timely fashion. Purpose The purpose of this project was to automate the adverse event reporting process, replacing paper-based processes with computer-based processes, so that personnel effort and time required for serious adverse event reporting was reduced, and the monitoring of reporting performance and adverse event characteristics was facilitated. Methods Use case analysis was employed to understand the reporting workflow and generate software requirements. The automation of the workflow was then implemented, employing computer databases, web-based forms, electronic signatures, and email communication. Results In the initial year (2007) of full deployment, 588 SAE reports were processed by the automated system, eSAEy™. The median time from initiation to Principal Investigator electronic signature was less than 2 days (mean 7 ± 0.7 days). This was a significant reduction from the prior paper-based system, which had a median time for signature of 24 days (mean of 45 ± 5.7 days). With eSAEy™, reports on adverse event characteristics (type, grade, etc.) were easily obtained and had consistent values based on standard terminologies. Limitation The automated system described was designed specifically for the work flow at Thomas Jefferson University. While the methodology for system design, and the system requirements derived from common clinical trials adverse reporting procedures are applicable in general, specific work flow details may not relevant at other institutions. Conclusion The system facilitated analysis of individual investigator reporting performance, as well as the aggregation and analysis of the nature of reported adverse

  10. Pre-implantation genetic diagnosis.

    PubMed

    Traeger-Synodinos, Joanne

    2017-02-01

    The aim of pre-implantation genetic diagnosis (PGD) is to characterize the genetic status of the cells (usually single cells) that have been biopsied from oocytes/zygotes or embryos created in vitro during assisted reproductive treatment. PGD is a multi-step procedure that requires close collaboration between gynaecologists who are experts in assisted reproduction, embryologists who are experts in micromanipulation of germ cells and in embryo biopsy and geneticists who are experts in genetic analysis at the single-cell level. PGD can be applied as a form of early pre-natal diagnosis with the aim to establish a pregnancy unaffected by a haemoglobinopathy. In addition, PGD can identify embryos that are human leukocyte antigen compatible with an existing sibling affected by a haemoglobinopathy to support a haematopoietic stem cell transplantation. PGD has an advantage over conventional pre-natal diagnosis as it precludes the need to consider terminating an affected ongoing pregnancy. However, PGD is a multi-step, complex and costly procedure with an unpredictable outcome and thus is most suited for couples with an unsuccessful reproductive history or challenging reproductive status. In addition, PGD supports the cure of an affected child. Couples who decide to undergo a PGD cycle should be fully aware of the advantages and limitations. The three teams of health practitioners involved (gynaecologists, embryologists and geneticists) should thoroughly counsel the couples and provide support at all the stages: the initial evaluation of their genetic and reproductive status, all steps of assisted reproduction, embryo biopsy, genetic analysis and, when relevant, follow-up of pregnancy and baby(ies) delivered. Copyright © 2016. Published by Elsevier Ltd.

  11. Automation synthesis modules review.

    PubMed

    Boschi, S; Lodi, F; Malizia, C; Cicoria, G; Marengo, M

    2013-06-01

    The introduction of (68)Ga labelled tracers has changed the diagnostic approach to neuroendocrine tumours and the availability of a reliable, long-lived (68)Ge/(68)Ga generator has been at the bases of the development of (68)Ga radiopharmacy. The huge increase in clinical demand, the impact of regulatory issues and a careful radioprotection of the operators have boosted for extensive automation of the production process. The development of automated systems for (68)Ga radiochemistry, different engineering and software strategies and post-processing of the eluate were discussed along with impact of automation with regulations. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Managing laboratory automation

    PubMed Central

    Saboe, Thomas J.

    1995-01-01

    This paper discusses the process of managing automated systems through their life cycles within the quality-control (QC) laboratory environment. The focus is on the process of directing and managing the evolving automation of a laboratory; system examples are given. The author shows how both task and data systems have evolved, and how they interrelate. A BIG picture, or continuum view, is presented and some of the reasons for success or failure of the various examples cited are explored. Finally, some comments on future automation need are discussed. PMID:18925018

  13. Single- and multistep selection study of the antipneumococcal activity of BMS-284756 compared to ciprofloxacin, levofloxacin, trovafloxacin and moxifloxacin.

    PubMed

    Clark, C L; Nagai, K; Davies, T A; Bozdogan, B; Dewasse, B; Jacobs, M R; Appelbaum, P C

    2002-06-01

    Single- and Multi-step selection studies were used to test the ability of BMS-284756, ciprofloxacin, levofloxacin, trovafloxacin and moxifloxacin to yield resistant clones from 12 quinolone-susceptible and -resistant Streptococcus pneumoniae strains. Although all quinolones selected, to a greater or lesser degree, for resistant clones with mutations usually in parC or gyrA, BMS-284756 tended to select for resistant clones at a lower rate than other quinolones studied.

  14. Fabrication of low-loss, single-mode-channel waveguide with DNA-CTMA biopolymer by multistep processing technology.

    PubMed

    Zhou, Jun; Wang, Zhen Yong; Yang, Xin; Wong, C-Y; Pun, Edwin Y B

    2010-05-15

    A multistep processing and reactive ion etching technique has been developed to fabricate optical channel waveguides based on deoxyribonucleic acid-cetyltrimethylammonium biopolymer material. The channel waveguides exhibit excellent single-mode output and high confinement of light because of the sharp waveguide profile with very smooth surfaces and vertical sidewalls. The measurement results show that these channel waveguides have low propagation losses and small polarization dependent losses at 633, 1310, and 1550 nm wavelengths.

  15. Cherenkov high-order harmonic generation by multistep cascading in {chi}{sup (2)} nonlinear photonic crystal

    SciTech Connect

    An Ning; Ren Huaijin; Zheng Yuanlin; Deng Xuewei; Chen Xianfeng

    2012-05-28

    We propose a scheme for efficient Cherenkov high-order harmonic generation. Second to fifth order harmonic wave are observed in a single periodically poled ferroelectric crystal in our experiment. The noncollinear high-order harmonic generation is produced via enhanced Cherenkov second harmonic cascaded with successive multistep sum-frequency generation with simultaneously longitudinal phase-matching. The emission angle and power dependencies are analyzed in detail experimentally, which coincide with theoretical predictions.

  16. Multistep modeling (MSM) of biomolecular structure application to the A-G mispair in the B-DNA environment

    NASA Technical Reports Server (NTRS)

    Srinivasan, S.; Raghunathan, G.; Shibata, M.; Rein, R.

    1986-01-01

    A multistep modeling procedure has been evolved to study the structural changes introduced by lesions in DNA. We report here the change in the structure of regular B-DNA geometry due to the incorporation of Ganti-Aanti mispair in place of a regular G-C pair, preserving the helix continuity. The energetics of the structure so obtained is compared with the Ganti-Asyn configuration under similar constrained conditions. We present the methodology adopted and discuss the results.

  17. A Family of Symmetric Linear Multistep Methods for the Numerical Solution of the Schroedinger Equation and Related Problems

    SciTech Connect

    Anastassi, Z. A.; Simos, T. E.

    2010-09-30

    We develop a new family of explicit symmetric linear multistep methods for the efficient numerical solution of the Schroedinger equation and related problems with oscillatory solution. The new methods are trigonometrically fitted and have improved intervals of periodicity as compared to the corresponding classical method with constant coefficients and other methods from the literature. We also apply the methods along with other known methods to real periodic problems, in order to measure their efficiency.

  18. Hippocampal-prefrontal theta phase synchrony in planning of multi-step actions based on memory retrieval.

    PubMed

    Ishino, Seiya; Takahashi, Susumu; Ogawa, Masaaki; Sakurai, Yoshio

    2017-02-23

    Planning of multi-step actions based on the retrieval of acquired information is essential for efficient foraging. The hippocampus (HPC) and prefrontal cortex (PFC) may play critical roles in this process. However, in rodents, many studies investigating such roles utilized T-maze tasks that only require one-step actions (i.e., selection of one of two alternatives), in which memory retrieval and selection of an action based on the retrieval cannot be clearly differentiated. In monkeys, PFC has been suggested to be involved in planning of multi-step actions; however, the synchrony between HPC and PFC has not been evaluated. To address the combined role of the regions in planning of multi-step actions, we introduced a task in rats that required three successive nose-poke responses to three sequentially illuminated nose-poke holes. During the task, local field potentials (LFP) and spikes from hippocampal CA1 and medial PFC (mPFC) were simultaneously recorded. The position of the first hole indicated whether the following two holes would be presented in a predictable sequence or not. During the first nose-poke period, phase synchrony of LFPs in the theta range (4-10 Hz) between the regions was not different between predictable and unpredictable trials. However, only in trials of predictable sequences, the magnitude of theta phase synchrony during the first nose-poke period was negatively correlated with latency of the two-step ahead nose-poke response. Our findings point to the HPC-mPFC theta phase synchrony as a key mechanism underlying planning of multi-step actions based on memory retrieval rather than the retrieval itself. This article is protected by copyright. All rights reserved.

  19. Multistep translation and cultural adaptation of the Penn acoustic neuroma quality-of-life scale for German-speaking patients.

    PubMed

    Kristin, Julia; Glaas, Marcel Fabian; Stenin, Igor; Albrecht, Angelika; Klenzner, Thomas; Schipper, Jörg; Eysel-Gosepath, Katrin

    2017-08-31

    Monitoring the health-related quality of life (HRQOL) for patients with vestibular schwannoma (VS) has garnered increasing interest. In German-speaking countries, there is no disease-specific questionnaire available similar to the "Penn Acoustic Neuroma Quality-of-life Scale" (PANQOL). We translated the PANQOL for German-speaking patients based on a multistep protocol that included not only a forward-backward translation but also linguistic and sociocultural adaptations. The process consists of translation, synthesis, back translation, review by an expert committee, administration of the prefinal version to our patients, submission and appraisal of all written documents by our research team. The required multidisciplinary team for translation comprised head and neck surgeons, language professionals (German and English), a professional translator, and bilingual participants. A total of 123 patients with VS underwent microsurgical procedures via different approaches at our clinic between January 2007 and January 2017. Among these, 72 patients who underwent the translabyrinthine approach participated in the testing of the German-translated PANQOL. The first German version of the PANQOL questionnaire was created by a multistep translation process. The responses indicate that the questionnaire is simple to administer and applicable to our patients. The use of a multistep process to translate quality-of-life questionnaires is complex and time-consuming. However, this process was performed properly and resulted in a version of the PANQOL for assessing the quality of life of German-speaking patients with VS.

  20. Multistep conversion of para-substituted phenols by phenol hydroxylase and 2,3-dihydroxybiphenyl 1,2-dioxygenase.

    PubMed

    Qu, Yuanyuan; Shi, Shengnan; Ma, Qiao; Kong, Chunlei; Zhou, Hao; Zhang, Xuwang; Zhou, Jiti

    2013-04-01

    A multistep conversion system of para-substituted phenols by recombinant phenol hydroxylase (PH(IND)) and 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC(LA-4)) was constructed in this study. Docking studies with different para-substituted phenols and corresponding catechols inside of the active site of PH(IND) and BphC(LA-4) predicted that all the substrates should be transformed. High-performance liquid chromatography-mass spectrometry analysis showed that the products of multistep conversion were the corresponding para-substituted catechols and semialdehydes. For the first-step conversion, the formation rate of 4-fluorocatechol (0.39 μM/min/mg dry weight) by strain PH(IND) hydroxylation was 1.15, 6.50, 3.00, and 1.18-fold higher than the formation of 4-chlorocatechol, 4-bromocatechol, 4-nitrocatechol, and 4-methylcatechol, respectively. For the second-step conversion, the formation rates of semialdehydes by strain BphC(LA-4) were as follows: 5-fluoro-HODA>5-chloro-HODA>2-hydroxy-5-nitro-ODA>5-bromo-HODA>2-hydroxy-5-methyl-ODA. The present study suggested that the multistep conversion by both ring hydroxylase and cleavage dioxygenase should be potential in the synthesis of industrial precursors and provide a novel avenue in the wastewater recycling treatment.

  1. Rapid on-chip multi-step (bio)chemical procedures in continuous flow--manoeuvring particles through co-laminar reagent streams.

    PubMed

    Peyman, Sally A; Iles, Alexander; Pamme, Nicole

    2008-03-14

    We introduce a novel and extremely versatile microfluidic platform in which tedious multi-step biochemical processes can be performed in continuous flow within a fraction of the time required for conventional methods.

  2. Xenon International Automated Control

    SciTech Connect

    2016-08-05

    The Xenon International Automated Control software monitors, displays status, and allows for manual operator control as well as fully automatic control of multiple commercial and PNNL designed hardware components to generate and transmit atmospheric radioxenon concentration measurements every six hours.

  3. Automating the Media Center.

    ERIC Educational Resources Information Center

    Holloway, Mary A.

    1988-01-01

    Discusses the need to develop more efficient information retrieval skills by the use of new technology. Lists four stages used in automating the media center. Describes North Carolina's pilot programs. Proposes benefits and looks at the media center's future. (MVL)

  4. Planning for Office Automation.

    ERIC Educational Resources Information Center

    Mick, Colin K.

    1983-01-01

    Outlines a practical approach to planning for office automation termed the "Focused Process Approach" (the "what" phase, "how" phase, "doing" phase) which is a synthesis of the problem-solving and participatory planning approaches. Thirteen references are provided. (EJS)

  5. Automated decision stations

    NASA Technical Reports Server (NTRS)

    Tischendorf, Mark

    1990-01-01

    This paper discusses the combination of software robots and expert systems to automate everyday business tasks. Tasks which require people to repetitively interact with multiple systems screens as well as multiple systems.

  6. DE-FG02-05ER64001 Overcoming the hurdles of multi-step targeting (MST) for effective radioimmunotherapy of solid tumors

    SciTech Connect

    P.I. Steven M. Larson MD Co P.I. Nai-Kong Cheung MD, Ph.D.

    2009-09-21

    The 4 specific aims of this project are: (1) Optimization of MST to increase tumor uptake; (2) Antigen heterogeneity; (3) Characterization and reduction of renal uptake; and (4) Validation in vivo of optimized MST targeted therapy. This proposal focussed upon optimizing multistep immune targeting strategies for the treatment of cancer. Two multi-step targeting constructs were explored during this funding period: (1) anti-Tag-72 and (2) anti-GD2.

  7. Automated Status Notification System

    NASA Technical Reports Server (NTRS)

    2005-01-01

    NASA Lewis Research Center's Automated Status Notification System (ASNS) was born out of need. To prevent "hacker attacks," Lewis' telephone system needed to monitor communications activities 24 hr a day, 7 days a week. With decreasing staff resources, this continuous monitoring had to be automated. By utilizing existing communications hardware, a UNIX workstation, and NAWK (a pattern scanning and processing language), we implemented a continuous monitoring system.

  8. Automated Microfluidics for Genomics

    DTIC Science & Technology

    2001-10-25

    Abstract--The Genomation Laboratory at the University of Washington is developing an automated fluid handling system called " Acapella " to prepare...Photonic Systems, Inc. (Redmond, WA), an automated submicroliter fluid sample preparation system called ACAPELLA is being developed. Reactions such...technology include minimal residual disease quantification and sample preparation for DNA. Preliminary work on the ACAPELLA is presented in [4][5]. This

  9. Automated Pilot Advisory System

    NASA Technical Reports Server (NTRS)

    Parks, J. L., Jr.; Haidt, J. G.

    1981-01-01

    An Automated Pilot Advisory System (APAS) was developed and operationally tested to demonstrate the concept that low cost automated systems can provide air traffic and aviation weather advisory information at high density uncontrolled airports. The system was designed to enhance the see and be seen rule of flight, and pilots who used the system preferred it over the self announcement system presently used at uncontrolled airports.

  10. Automating Index Preparation

    DTIC Science & Technology

    1987-03-23

    Automating Index Preparation* Pehong Chent Michael A. Harrison Computer Science Division University of CaliforniaI Berkeley, CA 94720 March 23, 1987...Abstract Index preparation is a tedious and time-consuming task. In this paper we indicate * how the indexing process can be automated in a way which...identified and analyzed. Specifically, we describe a framework for placing index commands in the document and a general purpose index processor which

  11. Automated Lattice Perturbation Theory

    SciTech Connect

    Monahan, Christopher

    2014-11-01

    I review recent developments in automated lattice perturbation theory. Starting with an overview of lattice perturbation theory, I focus on the three automation packages currently "on the market": HiPPy/HPsrc, Pastor and PhySyCAl. I highlight some recent applications of these methods, particularly in B physics. In the final section I briefly discuss the related, but distinct, approach of numerical stochastic perturbation theory.

  12. Metrology automation reliability

    NASA Astrophysics Data System (ADS)

    Chain, Elizabeth E.

    1996-09-01

    At Motorola's MOS-12 facility automated measurements on 200- mm diameter wafers proceed in a hands-off 'load-and-go' mode requiring only wafer loading, measurement recipe loading, and a 'run' command for processing. Upon completion of all sample measurements, the data is uploaded to the factory's data collection software system via a SECS II interface, eliminating the requirement of manual data entry. The scope of in-line measurement automation has been extended to the entire metrology scheme from job file generation to measurement and data collection. Data analysis and comparison to part specification limits is also carried out automatically. Successful integration of automated metrology into the factory measurement system requires that automated functions, such as autofocus and pattern recognition algorithms, display a high degree of reliability. In the 24- hour factory reliability data can be collected automatically on every part measured. This reliability data is then uploaded to the factory data collection software system at the same time as the measurement data. Analysis of the metrology reliability data permits improvements to be made as needed, and provides an accurate accounting of automation reliability. This reliability data has so far been collected for the CD-SEM (critical dimension scanning electron microscope) metrology tool, and examples are presented. This analysis method can be applied to such automated in-line measurements as CD, overlay, particle and film thickness measurements.

  13. Automated Groundwater Screening

    SciTech Connect

    Taylor, Glenn A.; Collard, Leonard, B.

    2005-10-31

    The Automated Intruder Analysis has been extended to include an Automated Ground Water Screening option. This option screens 825 radionuclides while rigorously applying the National Council on Radiation Protection (NCRP) methodology. An extension to that methodology is presented to give a more realistic screening factor for those radionuclides which have significant daughters. The extension has the promise of reducing the number of radionuclides which must be tracked by the customer. By combining the Automated Intruder Analysis with the Automated Groundwater Screening a consistent set of assumptions and databases is used. A method is proposed to eliminate trigger values by performing rigorous calculation of the screening factor thereby reducing the number of radionuclides sent to further analysis. Using the same problem definitions as in previous groundwater screenings, the automated groundwater screening found one additional nuclide, Ge-68, which failed the screening. It also found that 18 of the 57 radionuclides contained in NCRP Table 3.1 failed the screening. This report describes the automated groundwater screening computer application.

  14. Elements of EAF automation processes

    NASA Astrophysics Data System (ADS)

    Ioana, A.; Constantin, N.; Dragna, E. C.

    2017-01-01

    Our article presents elements of Electric Arc Furnace (EAF) automation. So, we present and analyze detailed two automation schemes: the scheme of electrical EAF automation system; the scheme of thermic EAF automation system. The application results of these scheme of automation consists in: the sensitive reduction of specific consummation of electrical energy of Electric Arc Furnace, increasing the productivity of Electric Arc Furnace, increase the quality of the developed steel, increasing the durability of the building elements of Electric Arc Furnace.

  15. Mouse Embryonic Stem Cells Inhibit Murine Cytomegalovirus Infection through a Multi-Step Process

    PubMed Central

    Kawasaki, Hideya; Kosugi, Isao; Arai, Yoshifumi; Iwashita, Toshihide; Tsutsui, Yoshihiro

    2011-01-01

    In humans, cytomegalovirus (CMV) is the most significant infectious cause of intrauterine infections that cause congenital anomalies of the central nervous system. Currently, it is not known how this process is affected by the timing of infection and the susceptibility of early-gestational-period cells. Embryonic stem (ES) cells are more resistant to CMV than most other cell types, although the mechanism responsible for this resistance is not well understood. Using a plaque assay and evaluation of immediate-early 1 mRNA and protein expression, we found that mouse ES cells were resistant to murine CMV (MCMV) at the point of transcription. In ES cells infected with MCMV, treatment with forskolin and trichostatin A did not confer full permissiveness to MCMV. In ES cultures infected with elongation factor-1α (EF-1α) promoter-green fluorescent protein (GFP) recombinant MCMV at a multiplicity of infection of 10, less than 5% of cells were GFP-positive, despite the fact that ES cells have relatively high EF-1α promoter activity. Quantitative PCR analysis of the MCMV genome showed that ES cells allow approximately 20-fold less MCMV DNA to enter the nucleus than mouse embryonic fibroblasts (MEFs) do, and that this inhibition occurs in a multi-step manner. In situ hybridization revealed that ES cell nuclei have significantly less MCMV DNA than MEF nuclei. This appears to be facilitated by the fact that ES cells express less heparan sulfate, β1 integrin, and vimentin, and have fewer nuclear pores, than MEF. This may reduce the ability of MCMV to attach to and enter through the cellular membrane, translocate to the nucleus, and cross the nuclear membrane in pluripotent stem cells (ES/induced pluripotent stem cells). The results presented here provide perspective on the relationship between CMV susceptibility and cell differentiation. PMID:21407806

  16. Two- and multi-step annealing of cereal starches in relation to gelatinization.

    PubMed

    Shi, Yong-Cheng

    2008-02-13

    Two- and multi-step annealing experiments were designed to determine how much gelatinization temperature of waxy rice, waxy barley, and wheat starches could be increased without causing a decrease in gelatinization enthalpy or a decline in X-ray crystallinity. A mixture of starch and excess water was heated in a differential scanning calorimeter (DSC) pan to a specific temperature and maintained there for 0.5-48 h. The experimental approach was first to anneal a starch at a low temperature so that the gelatinization temperature of the starch was increased without causing a decrease in gelatinization enthalpy. The annealing temperature was then raised, but still was kept below the onset gelatinization temperature of the previously annealed starch. When a second- or third-step annealing temperature was high enough, it caused a decrease in crystallinity, even though the holding temperature remained below the onset gelatinization temperature of the previously annealed starch. These results support that gelatinization is a nonequilibrium process and that dissociation of double helices is driven by the swelling of amorphous regions. Small-scale starch slurry annealing was also performed and confirmed the annealing results conducted in DSC pans. A three-phase model of a starch granule, a mobile amorphous phase, a rigid amorphous phase, and a crystalline phase, was used to interpret the annealing results. Annealing seems to be an interplay between a more efficient packing of crystallites in starch granules and swelling of plasticized amorphous regions. There is always a temperature ceiling that can be used to anneal a starch without causing a decrease in crystallinity. That temperature ceiling is starch-specific, dependent on the structure of a starch, and is lower than the original onset gelatinization of a starch.

  17. Comparability of river quality assessment using macrophytes: a multi-step procedure to overcome biogeographical differences.

    PubMed

    Aguiar, F C; Segurado, P; Urbanič, G; Cambra, J; Chauvin, C; Ciadamidaro, S; Dörflinger, G; Ferreira, J; Germ, M; Manolaki, P; Minciardi, M R; Munné, A; Papastergiadou, E; Ferreira, M T

    2014-04-01

    This paper exposes a new methodological approach to solve the problem of intercalibrating river quality national methods when a common metric is lacking and most of the countries share the same Water Framework Directive (WFD) assessment method. We provide recommendations for similar works in future concerning the assessment of ecological accuracy and highlight the importance of a good common ground to make feasible the scientific work beyond the intercalibration. The approach herein presented was applied to highly seasonal rivers of the Mediterranean Geographical Intercalibration Group for the Biological Quality Element Macrophytes. The Mediterranean Group of river macrophytes involved seven countries and two assessment methods with similar acquisition data and assessment concept: the Macrophyte Biological Index for Rivers (IBMR) for Cyprus, France, Greece, Italy, Portugal and Spain, and the River Macrophyte Index (RMI) for Slovenia. Database included 318 sites of which 78 were considered as benchmarks. The boundary harmonization was performed for common WFD-assessment methods (all countries except Slovenia) using the median of the Good/Moderate and High/Good boundaries of all countries. Then, whenever possible, the Slovenian method, RMI was computed for the entire database. The IBMR was also computed for the Slovenian sites and was regressed against RMI in order to check the relatedness of methods (R(2)=0.45; p<0.00001) and to convert RMI boundaries into the IBMR scale. The boundary bias of RMI was computed using direct comparison of classification and the median boundary values following boundary harmonization. The average absolute class differences after harmonization is 26% and the percentage of classifications differing by half of a quality class is also small (16.4%). This multi-step approach to the intercalibration was endorsed by the WFD Regulatory Committee. © 2013 Elsevier B.V. All rights reserved.

  18. Detection of Heterogeneous Small Inclusions by a Multi-Step MUSIC Method

    NASA Astrophysics Data System (ADS)

    Solimene, Raffaele; Dell'Aversano, Angela; Leone, Giovanni

    2014-05-01

    In this contribution the problem of detecting and localizing scatterers with small (in terms of wavelength) cross sections by collecting their scattered field is addressed. The problem is dealt with for a two-dimensional and scalar configuration where the background is given as a two-layered cylindrical medium. More in detail, while scattered field data are taken in the outermost layer, inclusions are embedded within the inner layer. Moreover, the case of heterogeneous inclusions (i.e., having different scattering coefficients) is addressed. As a pertinent applicative context we identify the problem of diagnose concrete pillars in order to detect and locate rebars, ducts and other small in-homogeneities that can populate the interior of the pillar. The nature of inclusions influences the scattering coefficients. For example, the field scattered by rebars is stronger than the one due to ducts. Accordingly, it is expected that the more weakly scattering inclusions can be difficult to be detected as their scattered fields tend to be overwhelmed by those of strong scatterers. In order to circumvent this problem, in this contribution a multi-step MUltiple SIgnal Classification (MUSIC) detection algorithm is adopted [1]. In particular, the first stage aims at detecting rebars. Once rebars have been detected, their positions are exploited to update the Green's function and to subtract the scattered field due to their presence. The procedure is repeated until all the inclusions are detected. The analysis is conducted by numerical experiments for a multi-view/multi-static single-frequency configuration and the synthetic data are generated by a FDTD forward solver. Acknowledgement This work benefited from networking activities carried out within the EU funded COST Action TU1208 "Civil Engineering Applications of Ground Penetrating Radar." [1] R. Solimene, A. Dell'Aversano and G. Leone, "MUSIC algorithms for rebar detection," J. of Geophysics and Engineering, vol. 10, pp. 1

  19. Kinetic analysis of overlapping multistep thermal decomposition comprising exothermic and endothermic processes: thermolysis of ammonium dinitramide.

    PubMed

    Muravyev, Nikita V; Koga, Nobuyoshi; Meerov, Dmitry B; Pivkina, Alla N

    2017-01-25

    This study focused on kinetic modeling of a specific type of multistep heterogeneous reaction comprising exothermic and endothermic reaction steps, as exemplified by the practical kinetic analysis of the experimental kinetic curves for the thermal decomposition of molten ammonium dinitramide (ADN). It is known that the thermal decomposition of ADN occurs as a consecutive two step mass-loss process comprising the decomposition of ADN and subsequent evaporation/decomposition of in situ generated ammonium nitrate. These reaction steps provide exothermic and endothermic contributions, respectively, to the overall thermal effect. The overall reaction process was deconvoluted into two reaction steps using simultaneously recorded thermogravimetry and differential scanning calorimetry (TG-DSC) curves by considering the different physical meanings of the kinetic data derived from TG and DSC by P value analysis. The kinetic data thus separated into exothermic and endothermic reaction steps were kinetically characterized using kinetic computation methods including isoconversional method, combined kinetic analysis, and master plot method. The overall kinetic behavior was reproduced as the sum of the kinetic equations for each reaction step considering the contributions to the rate data derived from TG and DSC. During reproduction of the kinetic behavior, the kinetic parameters and contributions of each reaction step were optimized using kinetic deconvolution analysis. As a result, the thermal decomposition of ADN was successfully modeled as partially overlapping exothermic and endothermic reaction steps. The logic of the kinetic modeling was critically examined, and the practical usefulness of phenomenological modeling for the thermal decomposition of ADN was illustrated to demonstrate the validity of the methodology and its applicability to similar complex reaction processes.

  20. On the Analysis of Multistep-Out-of-Grid Method for Celestial Mechanics Tasks

    NASA Astrophysics Data System (ADS)

    Olifer, L.; Choliy, V.

    2016-09-01

    Occasionally, there is a necessity in high-accurate prediction of celestial body trajectory. The most common way to do that is to solve Kepler's equation analytically or to use Runge-Kutta or Adams integrators to solve equation of motion numerically. For low-orbit satellites, there is a critical need in accounting geopotential and another forces which influence motion. As the result, the right side of equation of motion becomes much bigger, and classical integrators will not be quite effective. On the other hand, there is a multistep-out-of-grid (MOG) method which combines Runge-Kutta and Adams methods. The MOG method is based on using m on-grid values of the solution and n × m off-grid derivative estimations. Such method could provide stable integrators of maximum possible order, O (hm+mn+n-1). The main subject of this research was to implement and analyze the MOG method for solving satellite equation of motion with taking into account Earth geopotential model (ex. EGM2008 (Pavlis at al., 2008)) and with possibility to add other perturbations such as atmospheric drag or solar radiation pressure. Simulations were made for satellites on low orbit and with various eccentricities (from 0.1 to 0.9). Results of the MOG integrator were compared with results of Runge-Kutta and Adams integrators. It was shown that the MOG method has better accuracy than classical ones of the same order and less right-hand value estimations when is working on high orders. That gives it some advantage over "classical" methods.

  1. ALG: automated genotype calling of Luminex assays.

    PubMed

    Bourgey, Mathieu; Lariviere, Mathieu; Richer, Chantal; Sinnett, Daniel

    2011-05-06

    Single nucleotide polymorphisms (SNPs) are the most commonly used polymorphic markers in genetics studies. Among the different platforms for SNP genotyping, Luminex is one of the less exploited mainly due to the lack of a robust (semi-automated and replicable) freely available genotype calling software. Here we describe a clustering algorithm that provides automated SNP calls for Luminex genotyping assays. We genotyped 3 SNPs in a cohort of 330 childhood leukemia patients, 200 parents of patient and 325 healthy individuals and used the Automated Luminex Genotyping (ALG) algorithm for SNP calling. ALG genotypes were called twice to test for reproducibility and were compared to sequencing data to test for accuracy. Globally, this analysis demonstrates the accuracy (99.6%) of the method, its reproducibility (99.8%) and the low level of no genotyping calls (3.4%). The high efficiency of the method proves that ALG is a suitable alternative to the current commercial software. ALG is semi-automated, and provides numerical measures of confidence for each SNP called, as well as an effective graphical plot. Moreover ALG can be used either through a graphical user interface, requiring no specific informatics knowledge, or through command line with access to the open source code. The ALG software has been implemented in R and is freely available for non-commercial use either at http://alg.sourceforge.net or by request to mathieu.bourgey@umontreal.ca.

  2. Power subsystem automation study

    NASA Technical Reports Server (NTRS)

    Imamura, M. S.; Moser, R. L.; Veatch, M.

    1983-01-01

    Generic power-system elements and their potential faults are identified. Automation functions and their resulting benefits are defined and automation functions between power subsystem, central spacecraft computer, and ground flight-support personnel are partitioned. All automation activities were categorized as data handling, monitoring, routine control, fault handling, planning and operations, or anomaly handling. Incorporation of all these classes of tasks, except for anomaly handling, in power subsystem hardware and software was concluded to be mandatory to meet the design and operational requirements of the space station. The key drivers are long mission lifetime, modular growth, high-performance flexibility, a need to accommodate different electrical user-load equipment, onorbit assembly/maintenance/servicing, and potentially large number of power subsystem components. A significant effort in algorithm development and validation is essential in meeting the 1987 technology readiness date for the space station.

  3. Automated telescope scheduling

    NASA Astrophysics Data System (ADS)

    Johnston, Mark D.

    1988-08-01

    With the ever increasing level of automation of astronomical telescopes the benefits and feasibility of automated planning and scheduling are becoming more apparent. Improved efficiency and increased overall telescope utilization are the most obvious goals. Automated scheduling at some level has been done for several satellite observatories, but the requirements on these systems were much less stringent than on modern ground or satellite observatories. The scheduling problem is particularly acute for Hubble Space Telescope: virtually all observations must be planned in excruciating detail weeks to months in advance. Space Telescope Science Institute has recently made significant progress on the scheduling problem by exploiting state-of-the-art artificial intelligence software technology. What is especially interesting is that this effort has already yielded software that is well suited to scheduling groundbased telescopes, including the problem of optimizing the coordinated scheduling of more than one telescope.

  4. Automated telescope scheduling

    NASA Technical Reports Server (NTRS)

    Johnston, Mark D.

    1988-01-01

    With the ever increasing level of automation of astronomical telescopes the benefits and feasibility of automated planning and scheduling are becoming more apparent. Improved efficiency and increased overall telescope utilization are the most obvious goals. Automated scheduling at some level has been done for several satellite observatories, but the requirements on these systems were much less stringent than on modern ground or satellite observatories. The scheduling problem is particularly acute for Hubble Space Telescope: virtually all observations must be planned in excruciating detail weeks to months in advance. Space Telescope Science Institute has recently made significant progress on the scheduling problem by exploiting state-of-the-art artificial intelligence software technology. What is especially interesting is that this effort has already yielded software that is well suited to scheduling groundbased telescopes, including the problem of optimizing the coordinated scheduling of more than one telescope.

  5. Fully automated protein purification

    PubMed Central

    Camper, DeMarco V.; Viola, Ronald E.

    2009-01-01

    Obtaining highly purified proteins is essential to begin investigating their functional and structural properties. The steps that are typically involved in purifying proteins can include an initial capture, intermediate purification, and a final polishing step. Completing these steps can take several days and require frequent attention to ensure success. Our goal was to design automated protocols that will allow the purification of proteins with minimal operator intervention. Separate methods have been produced and tested that automate the sample loading, column washing, sample elution and peak collection steps for ion-exchange, metal affinity, hydrophobic interaction and gel filtration chromatography. These individual methods are designed to be coupled and run sequentially in any order to achieve a flexible and fully automated protein purification protocol. PMID:19595984

  6. Automated segmentation and reconstruction of patient-specific cardiac anatomy and pathology from in vivo MRI*

    NASA Astrophysics Data System (ADS)

    Ringenberg, Jordan; Deo, Makarand; Devabhaktuni, Vijay; Filgueiras-Rama, David; Pizarro, Gonzalo; Ibañez, Borja; Berenfeld, Omer; Boyers, Pamela; Gold, Jeffrey

    2012-12-01

    This paper presents an automated method to segment left ventricle (LV) tissues from functional and delayed-enhancement (DE) cardiac magnetic resonance imaging (MRI) scans using a sequential multi-step approach. First, a region of interest (ROI) is computed to create a subvolume around the LV using morphological operations and image arithmetic. From the subvolume, the myocardial contours are automatically delineated using difference of Gaussians (DoG) filters and GSV snakes. These contours are used as a mask to identify pathological tissues, such as fibrosis or scar, within the DE-MRI. The presented automated technique is able to accurately delineate the myocardium and identify the pathological tissue in patient sets. The results were validated by two expert cardiologists, and in one set the automated results are quantitatively and qualitatively compared with expert manual delineation. Furthermore, the method is patient-specific, performed on an entire patient MRI series. Thus, in addition to providing a quick analysis of individual MRI scans, the fully automated segmentation method is used for effectively tagging regions in order to reconstruct computerized patient-specific 3D cardiac models. These models can then be used in electrophysiological studies and surgical strategy planning.

  7. Disposable and removable nucleic acid extraction and purification cartridges for automated flow-through systems

    DOEpatents

    Regan, John Frederick

    2014-09-09

    Removable cartridges are used on automated flow-through systems for the purpose of extracting and purifying genetic material from complex matrices. Different types of cartridges are paired with specific automated protocols to concentrate, extract, and purifying pathogenic or human genetic material. Their flow-through nature allows large quantities sample to be processed. Matrices may be filtered using size exclusion and/or affinity filters to concentrate the pathogen of interest. Lysed material is ultimately passed through a filter to remove the insoluble material before the soluble genetic material is delivered past a silica-like membrane that binds the genetic material, where it is washed, dried, and eluted. Cartridges are inserted into the housing areas of flow-through automated instruments, which are equipped with sensors to ensure proper placement and usage of the cartridges. Properly inserted cartridges create fluid- and air-tight seals with the flow lines of an automated instrument.

  8. Automated gas chromatography

    DOEpatents

    Mowry, Curtis D.; Blair, Dianna S.; Rodacy, Philip J.; Reber, Stephen D.

    1999-01-01

    An apparatus and process for the continuous, near real-time monitoring of low-level concentrations of organic compounds in a liquid, and, more particularly, a water stream. A small liquid volume of flow from a liquid process stream containing organic compounds is diverted by an automated process to a heated vaporization capillary where the liquid volume is vaporized to a gas that flows to an automated gas chromatograph separation column to chromatographically separate the organic compounds. Organic compounds are detected and the information transmitted to a control system for use in process control. Concentrations of organic compounds less than one part per million are detected in less than one minute.

  9. Automation in optics manufacturing

    NASA Astrophysics Data System (ADS)

    Pollicove, Harvey M.; Moore, Duncan T.

    1991-01-01

    The optics industry has not followed the lead of the machining and electronics industries in applying advances in computer aided engineering (CAE), computer assisted manufacturing (CAM), automation or quality management techniques. Automation based on computer integrated manufacturing (CIM) and flexible machining systems (FMS) has been widely implemented in these industries. Optics continues to rely on standalone equipment that preserves the highly skilled, labor intensive optical fabrication systems developed in the 1940's. This paper describes development initiatives at the Center for Optics Manufacturing that will create computer integrated manufacturing technology and support processes for the optical industry.

  10. Automated software development workstation

    NASA Technical Reports Server (NTRS)

    1986-01-01

    Engineering software development was automated using an expert system (rule-based) approach. The use of this technology offers benefits not available from current software development and maintenance methodologies. A workstation was built with a library or program data base with methods for browsing the designs stored; a system for graphical specification of designs including a capability for hierarchical refinement and definition in a graphical design system; and an automated code generation capability in FORTRAN. The workstation was then used in a demonstration with examples from an attitude control subsystem design for the space station. Documentation and recommendations are presented.

  11. Automating the CMS DAQ

    SciTech Connect

    Bauer, G.; et al.

    2014-01-01

    We present the automation mechanisms that have been added to the Data Acquisition and Run Control systems of the Compact Muon Solenoid (CMS) experiment during Run 1 of the LHC, ranging from the automation of routine tasks to automatic error recovery and context-sensitive guidance to the operator. These mechanisms helped CMS to maintain a data taking efficiency above 90% and to even improve it to 95% towards the end of Run 1, despite an increase in the occurrence of single-event upsets in sub-detector electronics at high LHC luminosity.

  12. Automated Library System Specifications.

    DTIC Science & Technology

    1986-06-01

    AD-A78 95 AUTOMATED LIBRARY SYSTEM SPECIFICATIONS(U) ARMY LIBRARY /i MANAGEMENT OFFICE ALEXANDRIA VA ASSISTANT CHIEF OF STAFF FOR INFORMATION... MANAGEMENT M B BONNETT JUN 86 UNCLASSIFIED F/G 9/2 NLEElIIhllEEEEE IllEEEEEllllEI .1lm lliml * ~I fI.L25 MI, [OCM RL,;OCLUTO fl. ’N k~ AUTOMATED LIBRARY...SYSTEM SPECIFICATIONS .,I Prepared by Mary B. Bonnett ARMY LIBRARY MANAGEMENT OFFICE OFFICE OF THE ASSISTANT CHIEF OF STAFF FOR INFORMATION MANAGEMENT Lij

  13. Automated HMC assembly

    SciTech Connect

    Blazek, R.J.

    1993-08-01

    An automated gold wire bonder was characterized for bonding 1-mil gold wires to gallium-arsenide (GaAs) monolithic microwave integrated circuits (MMICs) which are used in microwave radar transmitter-receiver (T/R) modules. Acceptable gold wire bond test results were obtained for the fragile, 5-mil-thick GaAs MMICs with gold-metallized bond pads; and average wire bond pull strengths, shear strengths, and failure modes were determined. An automated aluminum wire bonder was modified to be used as a gold wire bonder so that a wedge bond capability was available for GaAs MMICs in addition to the gold ball bond capability.

  14. Automated knowledge generation

    NASA Technical Reports Server (NTRS)

    Myler, Harley R.; Gonzalez, Avelino J.

    1988-01-01

    The general objectives of the NASA/UCF Automated Knowledge Generation Project were the development of an intelligent software system that could access CAD design data bases, interpret them, and generate a diagnostic knowledge base in the form of a system model. The initial area of concentration is in the diagnosis of the process control system using the Knowledge-based Autonomous Test Engineer (KATE) diagnostic system. A secondary objective was the study of general problems of automated knowledge generation. A prototype was developed, based on object-oriented language (Flavors).

  15. Microtensile bond strength of new self-adhesive luting agents and conventional multistep systems.

    PubMed

    Viotti, Ronaldo G; Kasaz, Alline; Pena, Carlos E; Alexandre, Rodrigo S; Arrais, Cesar A; Reis, Andre F

    2009-11-01

    Several self-adhesive luting agents have recently been introduced on the market. It is crucial to know the effectiveness of such luting agents prior to their clinical application. The purpose of this study was to evaluate the microtensile bond strengths (microTBS) produced by different self-adhesive cements and compare them with conventional luting agents. Six self-adhesive cements (RelyX Unicem (UN), RelyX U100 (UC), SmartCem 2 (SC), G-Cem (GC), Maxcem (MC), and SeT (SET), and 2 conventional luting agents, one that uses a 2-step etch-and-rinse adhesive (RelyX ARC (RX)), and one that uses a 1-step self-etching adhesive (Panavia F (PF)), were used in this study. An additional group included the use of a 2-step self-etching primer adhesive system (Clearfil SE Bond) prior to the application of Panavia F (PS). Fifty-four human molars were abraded to expose occlusal surfaces and were assigned to 9 groups according to the luting material (n=6). Five composite resin (Filtek Z250) discs (12 mm in diameter, 5 mm thick) were cemented on the teeth according to manufacturers' instructions. After 24 hours of water storage, restored teeth were serially sectioned into beams with a cross-sectional area of approximately 1 mm2 at the bonded interface and were tested in tension with a crosshead speed of 1 mm/min. Failure mode was determined using scanning electron microscopy. Data were statistically analyzed by 1-way ANOVA and Tukey's studentized range HSD test (alpha =.05). Mean bond strengths (SD) in MPa were: RX, 69.6 (16.6)A; PS, 49.2 (9.7)A; PF, 33.7 (13.9)AB; GC, 16.9 (10.3)BC; UC, 15.3 (3.4)BC; UN, 12.5 (2.4)C; MC 11.5 (6.8)CD; SC, 8.5 (4.9)CD; SET, 4.6 (0.5)D. Groups with different uppercase letters were significantly different from each other (P<.05). The predominant failure mode of the self-adhesive cements was adhesive between the resin cement and dentin. The bond strengths produced by the multistep luting agents were significantly higher than those observed for most self

  16. A multistep algorithm for processing and calibration of microdialysis continuous glucose monitoring data.

    PubMed

    Mahmoudi, Zeinab; Dencker Johansen, Mette; Christiansen, Jens Sandahl; Hejlesen, Ole Kristian

    2013-10-01

    The deviation of continuous subcutaneous glucose monitoring (CGM) data from reference blood glucose measurements is substantial, and adequate signal processing is required to reduce the discrepancy between subcutaneous glucose and blood glucose values. The purpose of this study was to develop a multistep algorithm for the processing and calibration of continuous subcutaneous glucose monitoring data with high accuracy and short delay. Algorithm The algorithm comprises three steps: rate-limiting filtering, selective smoothing, and robust calibration. Initially, the algorithm detects nonphysiological glucose rate-of-change and corrects it with a weighted local polynomial. Noisy signal parts that require smoothing are then detected based on zero crossing count of the sensor signal first-order differences, and an exponentially weighted moving average smooths the noisy parts of the signal afterward. Finally, calibration is performed using a first-order polynomial as the conversion function, with coefficients being estimated using robust regression with a bi-square weight function. ALGORITHM PERFORMANCE: The performance of the algorithm was evaluated on 16 patients with type 1 diabetes mellitus. To compare the algorithm with state-of-the-art CGM data denoising and calibration, the rate-limiting filter and selective smoothing were replaced with an adaptive Kalman filter, and the calibration method was replaced with the calibration algorithm presented in one of the Medtronic (Northridge, CA) CGM patents. The median (mean) of the absolute relative deviation (ARD) of the sensor glucose values processed by the newly developed algorithm from capillary reference blood glucose measurements was 14.8% (22.6%), 10.6% (14.6%), and 8.9% (11.7%) in hypoglycemia, euglycemia, and hyperglycemia, respectively, whereas for the alternative algorithm, the median (mean) was 22.2% (26.9%), 12.1% (15.9%), and 8.8 (11.3%), respectively. The median (mean) ARD in all ranges was 10.3% (14.7%) for

  17. Achieving effective terminal exciton delivery in quantum dot antenna-sensitized multistep DNA photonic wires.

    PubMed

    Spillmann, Christopher M; Ancona, Mario G; Buckhout-White, Susan; Algar, W Russ; Stewart, Michael H; Susumu, Kimihiro; Huston, Alan L; Goldman, Ellen R; Medintz, Igor L

    2013-08-27

    exciton transfer efficiencies approaching 100% are seen when the dye spacings are 0.5 × R0. However, as additional dyes are included in each wire, strong nonidealities appear that are suspected to arise predominantly from the poor photophysical performance of the last two acceptor dyes (Cy5 and Cy5.5). The results are discussed in the context of improving exciton transfer efficiency along photonic wires and the contributions these architectures can make to understanding multistep FRET processes.

  18. Analysis of amyotrophic lateral sclerosis as a multistep process: a population-based modelling study

    PubMed Central

    Al-Chalabi, Ammar; Calvo, Andrea; Chio, Adriano; Colville, Shuna; Ellis, Cathy M; Hardiman, Orla; Heverin, Mark; Howard, Robin S; Huisman, Mark H B; Keren, Noa; Leigh, P Nigel; Mazzini, Letizia; Mora, Gabriele; Orrell, Richard W; Rooney, James; Scott, Kirsten M; Scotton, William J; Seelen, Meinie; Shaw, Christopher E; Sidle, Katie S; Swingler, Robert; Tsuda, Miho; Veldink, Jan H; Visser, Anne E; van den Berg, Leonard H; Pearce, Neil

    2014-01-01

    Summary Background Amyotrophic lateral sclerosis shares characteristics with some cancers, such as onset being more common in later life, progression usually being rapid, the disease affecting a particular cell type, and showing complex inheritance. We used a model originally applied to cancer epidemiology to investigate the hypothesis that amyotrophic lateral sclerosis is a multistep process. Methods We generated incidence data by age and sex from amyotrophic lateral sclerosis population registers in Ireland (registration dates 1995–2012), the Netherlands (2006–12), Italy (1995–2004), Scotland (1989–98), and England (2002–09), and calculated age and sex-adjusted incidences for each register. We regressed the log of age-specific incidence against the log of age with least squares regression. We did the analyses within each register, and also did a combined analysis, adjusting for register. Findings We identified 6274 cases of amyotrophic lateral sclerosis from a catchment population of about 34 million people. We noted a linear relationship between log incidence and log age in all five registers: England r2=0·95, Ireland r2=0·99, Italy r2=0·95, the Netherlands r2=0·99, and Scotland r2=0·97; overall r2=0·99. All five registers gave similar estimates of the linear slope ranging from 4·5 to 5·1, with overlapping confidence intervals. The combination of all five registers gave an overall slope of 4·8 (95% CI 4·5–5·0), with similar estimates for men (4·6, 4·3–4·9) and women (5·0, 4·5–5·5). Interpretation A linear relationship between the log incidence and log age of onset of amyotrophic lateral sclerosis is consistent with a multistage model of disease. The slope estimate suggests that amyotrophic lateral sclerosis is a six-step process. Identification of these steps could lead to preventive and therapeutic avenues. Funding UK Medical Research Council; UK Economic and Social Research Council; Ireland Health Research Board; The

  19. Analysis of amyotrophic lateral sclerosis as a multistep process: a population-based modelling study.

    PubMed

    Al-Chalabi, Ammar; Calvo, Andrea; Chio, Adriano; Colville, Shuna; Ellis, Cathy M; Hardiman, Orla; Heverin, Mark; Howard, Robin S; Huisman, Mark H B; Keren, Noa; Leigh, P Nigel; Mazzini, Letizia; Mora, Gabriele; Orrell, Richard W; Rooney, James; Scott, Kirsten M; Scotton, William J; Seelen, Meinie; Shaw, Christopher E; Sidle, Katie S; Swingler, Robert; Tsuda, Miho; Veldink, Jan H; Visser, Anne E; van den Berg, Leonard H; Pearce, Neil

    2014-11-01

    Amyotrophic lateral sclerosis shares characteristics with some cancers, such as onset being more common in later life, progression usually being rapid, the disease affecting a particular cell type, and showing complex inheritance. We used a model originally applied to cancer epidemiology to investigate the hypothesis that amyotrophic lateral sclerosis is a multistep process. We generated incidence data by age and sex from amyotrophic lateral sclerosis population registers in Ireland (registration dates 1995-2012), the Netherlands (2006-12), Italy (1995-2004), Scotland (1989-98), and England (2002-09), and calculated age and sex-adjusted incidences for each register. We regressed the log of age-specific incidence against the log of age with least squares regression. We did the analyses within each register, and also did a combined analysis, adjusting for register. We identified 6274 cases of amyotrophic lateral sclerosis from a catchment population of about 34 million people. We noted a linear relationship between log incidence and log age in all five registers: England r(2)=0·95, Ireland r(2)=0·99, Italy r(2)=0·95, the Netherlands r(2)=0·99, and Scotland r(2)=0·97; overall r(2)=0·99. All five registers gave similar estimates of the linear slope ranging from 4·5 to 5·1, with overlapping confidence intervals. The combination of all five registers gave an overall slope of 4·8 (95% CI 4·5-5·0), with similar estimates for men (4·6, 4·3-4·9) and women (5·0, 4·5-5·5). A linear relationship between the log incidence and log age of onset of amyotrophic lateral sclerosis is consistent with a multistage model of disease. The slope estimate suggests that amyotrophic lateral sclerosis is a six-step process. Identification of these steps could lead to preventive and therapeutic avenues. UK Medical Research Council; UK Economic and Social Research Council; Ireland Health Research Board; The Netherlands Organisation for Health Research and Development (ZonMw); the

  20. Transarterial chemoembolization using iodized oil for unresectable hepatocellular carcinoma: perspective from multistep hepatocarcinogenesis.

    PubMed

    Yoshimitsu, Kengo

    2014-01-01

    Transarterial chemoembolization (TACE) using iodized oil (Lipiodol(®)) (Lp-TACE) as a carrier of chemotherapeutic agents has been routinely performed to control hepatocellular carcinomas (HCC) in Japan, and its use has yielded fairly beneficial therapeutic results. Lipiodol is thought to pass through the tumor sinusoids of HCC and reach the outflow drainage areas, namely, the portal venous side of the tumor. By doing this, Lipiodol blocks not only the tumor's arterial inflow but also its portal venous outflow, providing sufficient ischemic effects. It is known that the inflow blood system, tumor sinusoids, and outflow blood system change drastically during the process of multistep hepatocarcinogenesis; thus, it is reasonable to postulate that the distribution of Lipiodol and the subsequent therapeutic effect of Lp-TACE may also change during that process. Arterial inflow to HCC is highest for moderately differentiated HCC (mHCC) and is relatively low in well or poorly differentiated HCC (wHCC and pHCC, respectively). It has been suggested that the metabolic state of wHCC and mHCC is aerobic, while that of pHCC is anaerobic. The tumor sinusoids in wHCC and mHCC are small in size and large in number, while those in pHCC are large in size and small in number. This finding results in a greater chance of tumor cell exposure to chemotherapeutic agents in the former and a lesser chance in the latter. The outflow tract, namely, the drainage system via the residual portal venous branches within the pseudocapsule, is more complete in mHCC and pHCC and less so in wHCC. Considering all of these components of HCC of different histological grades, Lp-TACE should have the greatest effect on mHCC and a relatively low effect on wHCC and pHCC. To achieve consistently high therapeutic results, it is important to consider these components, which affect the sensitivity of HCC to Lp-TACE, to maximize both the chemotherapeutic and ischemic effects of this therapy.

  1. Multi-steps infrared spectroscopic characterization of the effect of flowering on medicinal value of Cistanche tubulosa

    NASA Astrophysics Data System (ADS)

    Lai, Zuliang; Xu, Peng; Wu, Peiyi

    2009-01-01

    Multi-steps infrared spectroscopic methods, including conventional Fourier transform infrared spectroscopy (FT-IR), second derivative spectroscopy and two-dimensional infrared (2D-IR) correlation spectroscopy, have been proved to be effective methods to examine complicated mixture system such as Chinese herbal medicine. The focus of this paper is the investigation on the effect of flowering on the pharmaceutical components of Cistanche tubulosa by using the Multi-steps infrared spectroscopic method. Power-spectrum analysis is applied to improve the resolution of 2D-IR contour maps and much more details of overlapped peaks are detected. According to the results of FT-IR and second derivative spectra, the peak at 1732 cm -1 assigned to C dbnd O is stronger before flowering than that after flowering in the stem, while more C dbnd O groups are found in the top after flowering. The spectra of root change a lot in the process of flowering for the reason that many peaks shift and disappear after flowering. Seven peaks in the spectra of stem, which are assigned to different kinds of glycoside components, are distinguished by Power-spectra in the range of 900-1200 cm -1. The results provide a scientific explanation to the traditional experience that flowering consumes the pharmaceutical components in stem and the seeds absorb some nutrients of stem after flowering. In conclusion, the Multi-steps infrared spectroscopic method combined with Power-spectra is a promising method to investigate the flowering process of C. tubulosa and discriminate various parts of the herbal medicine.

  2. Altering user' acceptance of automation through prior automation exposure.

    PubMed

    Bekier, Marek; Molesworth, Brett R C

    2016-08-22

    Air navigation service providers worldwide see increased use of automation as one solution to overcome the capacity constraints imbedded in the present air traffic management (ATM) system. However, increased use of automation within any system is dependent on user acceptance. The present research sought to determine if the point at which an individual is no longer willing to accept or cooperate with automation can be manipulated. Forty participants underwent training on a computer-based air traffic control programme, followed by two ATM exercises (order counterbalanced), one with and one without the aid of automation. Results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation ('tipping point') decreased; suggesting it is indeed possible to alter automation acceptance. Practitioner Summary: This paper investigates whether the point at which a user of automation rejects automation (i.e. 'tipping point') is constant or can be manipulated. The results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation decreased; suggesting it is possible to alter automation acceptance.

  3. Multi-Step Ka/Ka Dichroic Plate with Rounded Corners for NASA's 34m Beam Waveguide Antenna

    NASA Technical Reports Server (NTRS)

    Veruttipong, Watt; Khayatian, Behrouz; Hoppe, Daniel; Long, Ezra

    2013-01-01

    A multi-step Ka/Ka dichroic plate Frequency Selective Surface (FSS structure) is designed, manufactured and tested for use in NASA's Deep Space Network (DSN) 34m Beam Waveguide (BWG) antennas. The proposed design allows ease of manufacturing and ability to handle the increased transmit power (reflected off the FSS) of the DSN BWG antennas from 20kW to 100 kW. The dichroic is designed using HFSS and results agree well with measured data considering the manufacturing tolerances that could be achieved on the dichroic.

  4. Multi-Step Ka/Ka Dichroic Plate with Rounded Corners for NASA's 34m Beam Waveguide Antenna

    NASA Technical Reports Server (NTRS)

    Veruttipong, Watt; Khayatian, Behrouz; Hoppe, Daniel; Long, Ezra

    2013-01-01

    A multi-step Ka/Ka dichroic plate Frequency Selective Surface (FSS structure) is designed, manufactured and tested for use in NASA's Deep Space Network (DSN) 34m Beam Waveguide (BWG) antennas. The proposed design allows ease of manufacturing and ability to handle the increased transmit power (reflected off the FSS) of the DSN BWG antennas from 20kW to 100 kW. The dichroic is designed using HFSS and results agree well with measured data considering the manufacturing tolerances that could be achieved on the dichroic.

  5. Investigation and comparison of analytical, numerical, and experimentally measured coupling losses for multi-step index optical fibers.

    PubMed

    Aldabaldetreku, Gotzon; Durana, Gaizka; Zubia, Joseba; Arrue, Jon; Poisel, Hans; Losada, María

    2005-05-30

    The aim of the present paper is to provide a comprehensive analysis of the coupling losses in multi-step index (MSI) fibres. Their light power acceptance properties are investigated to obtain the corresponding analytical expressions taking into account longitudinal, transverse, and angular misalignments. For this purpose, a uniform power distribution is assumed. In addition, we perform several experimental measurements and computer simulations in order to calculate the coupling losses for two different MSI polymer optical fibres (MSI-POFs). These results serve us to validate the theoretical expressions we have obtained.

  6. Human Factors In Aircraft Automation

    NASA Technical Reports Server (NTRS)

    Billings, Charles

    1995-01-01

    Report presents survey of state of art in human factors in automation of aircraft operation. Presents examination of aircraft automation and effects on flight crews in relation to human error and aircraft accidents.

  7. Automated measurement of Drosophila wings.

    PubMed

    Houle, David; Mezey, Jason; Galpern, Paul; Carter, Ashley

    2003-12-11

    Many studies in evolutionary biology and genetics are limited by the rate at which phenotypic information can be acquired. The wings of Drosophila species are a favorable target for automated analysis because of the many interesting questions in evolution and development that can be addressed with them, and because of their simple structure. We have developed an automated image analysis system (WINGMACHINE) that measures the positions of all the veins and the edges of the wing blade of Drosophilid flies. A video image is obtained with the aid of a simple suction device that immobilizes the wing of a live fly. Low-level processing is used to find the major intersections of the veins. High-level processing then optimizes the fit of an a priori B-spline model of wing shape. WINGMACHINE allows the measurement of 1 wing per minute, including handling, imaging, analysis, and data editing. The repeatabilities of 12 vein intersections averaged 86% in a sample of flies of the same species and sex. Comparison of 2400 wings of 25 Drosophilid species shows that wing shape is quite conservative within the group, but that almost all taxa are diagnosably different from one another. Wing shape retains some phylogenetic structure, although some species have shapes very different from closely related species. The WINGMACHINE system facilitates artificial selection experiments on complex aspects of wing shape. We selected on an index which is a function of 14 separate measurements of each wing. After 14 generations, we achieved a 15 S.D. difference between up and down-selected treatments. WINGMACHINE enables rapid, highly repeatable measurements of wings in the family Drosophilidae. Our approach to image analysis may be applicable to a variety of biological objects that can be represented as a framework of connected lines.

  8. Automated Management Of Documents

    NASA Technical Reports Server (NTRS)

    Boy, Guy

    1995-01-01

    Report presents main technical issues involved in computer-integrated documentation. Problems associated with automation of management and maintenance of documents analyzed from perspectives of artificial intelligence and human factors. Technologies that may prove useful in computer-integrated documentation reviewed: these include conventional approaches to indexing and retrieval of information, use of hypertext, and knowledge-based artificial-intelligence systems.

  9. Guide to Library Automation.

    ERIC Educational Resources Information Center

    Toohill, Barbara G.

    Directed toward librarians and library administrators who wish to procure automated systems or services for their libraries, this guide offers practical suggestions, advice, and methods for determining requirements, estimating costs and benefits, writing specifications procuring systems, negotiating contracts, and installing systems. The advice…

  10. Automated Management Of Documents

    NASA Technical Reports Server (NTRS)

    Boy, Guy

    1995-01-01

    Report presents main technical issues involved in computer-integrated documentation. Problems associated with automation of management and maintenance of documents analyzed from perspectives of artificial intelligence and human factors. Technologies that may prove useful in computer-integrated documentation reviewed: these include conventional approaches to indexing and retrieval of information, use of hypertext, and knowledge-based artificial-intelligence systems.

  11. Microcontroller for automation application

    NASA Technical Reports Server (NTRS)

    Cooper, H. W.

    1975-01-01

    The description of a microcontroller currently being developed for automation application was given. It is basically an 8-bit microcomputer with a 40K byte random access memory/read only memory, and can control a maximum of 12 devices through standard 15-line interface ports.

  12. Building Automation Systems.

    ERIC Educational Resources Information Center

    Honeywell, Inc., Minneapolis, Minn.

    A number of different automation systems for use in monitoring and controlling building equipment are described in this brochure. The system functions include--(1) collection of information, (2) processing and display of data at a central panel, and (3) taking corrective action by sounding alarms, making adjustments, or automatically starting and…

  13. Automated Estimating System (AES)

    SciTech Connect

    Holder, D.A.

    1989-09-01

    This document describes Version 3.1 of the Automated Estimating System, a personal computer-based software package designed to aid in the creation, updating, and reporting of project cost estimates for the Estimating and Scheduling Department of the Martin Marietta Energy Systems Engineering Division. Version 3.1 of the Automated Estimating System is capable of running in a multiuser environment across a token ring network. The token ring network makes possible services and applications that will more fully integrate all aspects of information processing, provides a central area for large data bases to reside, and allows access to the data base by multiple users. Version 3.1 of the Automated Estimating System also has been enhanced to include an Assembly pricing data base that may be used to retrieve cost data into an estimate. A WBS Title File program has also been included in Version 3.1. The WBS Title File program allows for the creation of a WBS title file that has been integrated with the Automated Estimating System to provide WBS titles in update mode and in reports. This provides for consistency in WBS titles and provides the capability to display WBS titles on reports generated at a higher WBS level.

  14. Automated Essay Scoring

    ERIC Educational Resources Information Center

    Dikli, Semire

    2006-01-01

    The impacts of computers on writing have been widely studied for three decades. Even basic computers functions, i.e. word processing, have been of great assistance to writers in modifying their essays. The research on Automated Essay Scoring (AES) has revealed that computers have the capacity to function as a more effective cognitive tool (Attali,…

  15. Automated Microbial Genome Annotation

    SciTech Connect

    Land, Miriam

    2009-05-29

    Miriam Land of the DOE Joint Genome Institute at Oak Ridge National Laboratory gives a talk on the current state and future challenges of moving toward automated microbial genome annotation at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  16. Building Automation Systems.

    ERIC Educational Resources Information Center

    Honeywell, Inc., Minneapolis, Minn.

    A number of different automation systems for use in monitoring and controlling building equipment are described in this brochure. The system functions include--(1) collection of information, (2) processing and display of data at a central panel, and (3) taking corrective action by sounding alarms, making adjustments, or automatically starting and…

  17. Automated Tendering and Purchasing.

    ERIC Educational Resources Information Center

    DeZorzi, James M.

    1980-01-01

    The Middlesex County Board of Education in Hyde Park (Ontario) has developed an automated tendering/purchasing system for ordering standard items that has reduced by 80 percent the time required for tendering, evaluating, awarding, and ordering items. (Author/MLF)

  18. Automated conflict resolution issues

    NASA Technical Reports Server (NTRS)

    Wike, Jeffrey S.

    1991-01-01

    A discussion is presented of how conflicts for Space Network resources should be resolved in the ATDRSS era. The following topics are presented: a description of how resource conflicts are currently resolved; a description of issues associated with automated conflict resolution; present conflict resolution strategies; and topics for further discussion.

  19. ATC automation concepts

    NASA Technical Reports Server (NTRS)

    Erzberger, Heinz

    1990-01-01

    Information on the design of human-centered tools for terminal area air traffic control (ATC) is given in viewgraph form. Information is given on payoffs and products, guidelines, ATC as a team process, automation tools for ATF, and the traffic management advisor.

  20. Automated Administrative Data Bases

    NASA Technical Reports Server (NTRS)

    Marrie, M. D.; Jarrett, J. R.; Reising, S. A.; Hodge, J. E.

    1984-01-01

    Improved productivity and more effective response to information requirements for internal management, NASA Centers, and Headquarters resulted from using automated techniques. Modules developed to provide information on manpower, RTOPS, full time equivalency, and physical space reduced duplication, increased communication, and saved time. There is potential for greater savings by sharing and integrating with those who have the same requirements.

  1. Automating Small Libraries.

    ERIC Educational Resources Information Center

    Swan, James

    1996-01-01

    Presents a four-phase plan for small libraries strategizing for automation: inventory and weeding, data conversion, implementation, and enhancements. Other topics include selecting a system, MARC records, compatibility, ease of use, industry standards, searching capabilities, support services, system security, screen displays, circulation modules,…

  2. Automated Lumber Processing

    Treesearch

    Powsiri Klinkhachorn; J. Moody; Philip A. Araman

    1995-01-01

    For the past few decades, researchers have devoted time and effort to apply automation and modern computer technologies towards improving the productivity of traditional industries. To be competitive, one must streamline operations and minimize production costs, while maintaining an acceptable margin of profit. This paper describes the effort of one such endeavor...

  3. Personnel Department Automation.

    ERIC Educational Resources Information Center

    Wilkinson, David

    In 1989, the Austin Independent School District's Office of Research and Evaluation was directed to monitor the automation of personnel information and processes in the district's Department of Personnel. Earlier, a study committee appointed by the Superintendent during the 1988-89 school year identified issues related to Personnel Department…

  4. Automated Accounting. Instructor Guide.

    ERIC Educational Resources Information Center

    Moses, Duane R.

    This curriculum guide was developed to assist business instructors using Dac Easy Accounting College Edition Version 2.0 software in their accounting programs. The module consists of four units containing assignment sheets and job sheets designed to enable students to master competencies identified in the area of automated accounting. The first…

  5. Automated Student Model Improvement

    ERIC Educational Resources Information Center

    Koedinger, Kenneth R.; McLaughlin, Elizabeth A.; Stamper, John C.

    2012-01-01

    Student modeling plays a critical role in developing and improving instruction and instructional technologies. We present a technique for automated improvement of student models that leverages the DataShop repository, crowd sourcing, and a version of the Learning Factors Analysis algorithm. We demonstrate this method on eleven educational…

  6. Validating Automated Speaking Tests

    ERIC Educational Resources Information Center

    Bernstein, Jared; Van Moere, Alistair; Cheng, Jian

    2010-01-01

    This paper presents evidence that supports the valid use of scores from fully automatic tests of spoken language ability to indicate a person's effectiveness in spoken communication. The paper reviews the constructs, scoring, and the concurrent validity evidence of "facility-in-L2" tests, a family of automated spoken language tests in Spanish,…

  7. Automated EEG acquisition

    NASA Technical Reports Server (NTRS)

    Frost, J. D., Jr.; Hillman, C. E., Jr.

    1977-01-01

    Automated self-contained portable device can be used by technicians with minimal training. Data acquired from patient at remote site are transmitted to centralized interpretation center using conventional telephone equipment. There, diagnostic information is analyzed, and results are relayed back to remote site.

  8. Automated Inadvertent Intruder Application

    SciTech Connect

    Koffman, Larry D.; Lee, Patricia L.; Cook, James R.; Wilhite, Elmer L.

    2008-01-15

    The Environmental Analysis and Performance Modeling group of Savannah River National Laboratory (SRNL) conducts performance assessments of the Savannah River Site (SRS) low-level waste facilities to meet the requirements of DOE Order 435.1. These performance assessments, which result in limits on the amounts of radiological substances that can be placed in the waste disposal facilities, consider numerous potential exposure pathways that could occur in the future. One set of exposure scenarios, known as inadvertent intruder analysis, considers the impact on hypothetical individuals who are assumed to inadvertently intrude onto the waste disposal site. Inadvertent intruder analysis considers three distinct scenarios for exposure referred to as the agriculture scenario, the resident scenario, and the post-drilling scenario. Each of these scenarios has specific exposure pathways that contribute to the overall dose for the scenario. For the inadvertent intruder analysis, the calculation of dose for the exposure pathways is a relatively straightforward algebraic calculation that utilizes dose conversion factors. Prior to 2004, these calculations were performed using an Excel spreadsheet. However, design checks of the spreadsheet calculations revealed that errors could be introduced inadvertently when copying spreadsheet formulas cell by cell and finding these errors was tedious and time consuming. This weakness led to the specification of functional requirements to create a software application that would automate the calculations for inadvertent intruder analysis using a controlled source of input parameters. This software application, named the Automated Inadvertent Intruder Application, has undergone rigorous testing of the internal calculations and meets software QA requirements. The Automated Inadvertent Intruder Application was intended to replace the previous spreadsheet analyses with an automated application that was verified to produce the same calculations and

  9. Automating spectral measurements

    NASA Astrophysics Data System (ADS)

    Goldstein, Fred T.

    2008-09-01

    This paper discusses the architecture of software utilized in spectroscopic measurements. As optical coatings become more sophisticated, there is mounting need to automate data acquisition (DAQ) from spectrophotometers. Such need is exacerbated when 100% inspection is required, ancillary devices are utilized, cost reduction is crucial, or security is vital. While instrument manufacturers normally provide point-and-click DAQ software, an application programming interface (API) may be missing. In such cases automation is impossible or expensive. An API is typically provided in libraries (*.dll, *.ocx) which may be embedded in user-developed applications. Users can thereby implement DAQ automation in several Windows languages. Another possibility, developed by FTG as an alternative to instrument manufacturers' software, is the ActiveX application (*.exe). ActiveX, a component of many Windows applications, provides means for programming and interoperability. This architecture permits a point-and-click program to act as automation client and server. Excel, for example, can control and be controlled by DAQ applications. Most importantly, ActiveX permits ancillary devices such as barcode readers and XY-stages to be easily and economically integrated into scanning procedures. Since an ActiveX application has its own user-interface, it can be independently tested. The ActiveX application then runs (visibly or invisibly) under DAQ software control. Automation capabilities are accessed via a built-in spectro-BASIC language with industry-standard (VBA-compatible) syntax. Supplementing ActiveX, spectro-BASIC also includes auxiliary serial port commands for interfacing programmable logic controllers (PLC). A typical application is automatic filter handling.

  10. Rapid access to compound libraries through flow technology: fully automated synthesis of a 3-aminoindolizine library via orthogonal diversification.

    PubMed

    Lange, Paul P; James, Keith

    2012-10-08

    A novel methodology for the synthesis of druglike heterocycle libraries has been developed through the use of flow reactor technology. The strategy employs orthogonal modification of a heterocyclic core, which is generated in situ, and was used to construct both a 25-membered library of druglike 3-aminoindolizines, and selected examples of a 100-member virtual library. This general protocol allows a broad range of acylation, alkylation and sulfonamidation reactions to be performed in conjunction with a tandem Sonogashira coupling/cycloisomerization sequence. All three synthetic steps were conducted under full automation in the flow reactor, with no handling or isolation of intermediates, to afford the desired products in good yields. This fully automated, multistep flow approach opens the way to highly efficient generation of druglike heterocyclic systems as part of a lead discovery strategy or within a lead optimization program.

  11. Multi-step plasma etching process for development of highly photosensitive InSb mid-IR FPAs

    NASA Astrophysics Data System (ADS)

    Seok, Chulkyun; Choi, Minkyung; Yang, In-Sang; Park, Sehun; Park, Yongjo; Yoon, Euijoon

    2014-06-01

    Reactive ion beam etching (RIBE) with CH4/H2/Ar or Cl2/Ar and ion beam etching (IBE) with Ar has been widely used for indium-contained compound semiconductors such as InAs, InP and InSb. To improve the performance of InSb FPAs, reduction of the ion-induced defects and the surface roughness is one of the key issues. To find the optimized plasma etching method for the fabrication of InSb devices, conventional plasma etching processes were comparatively investigated. RIBE of InSb was observed to generate residual by-products such as carbide and chloride causing the degradation of devices. On the other hand, very smooth surface was obtained by etching with N2. However, the etch rate of the N2 etching was too slow for the application to the device fabrication. As an alternative way to solve these problems, a multi-step plasma etching process, a combination of the Ar etching and the N2 etching, for InSb was developed. As gradually increasing the amount of N2 gas flow during the etching process, the plasma damage causing the surface roughen decreased and consequently smoother surface close to that of N2 RIE could be obtained. Furthermore, Raman analysis of the InSb surface after the plasma etching indicated clearly that the multi-step etching process was an effective approach in reducing the ion-induced damages on the surface.

  12. Fabrication of different pore shapes by multi-step etching technique in ion-irradiated PET membranes

    NASA Astrophysics Data System (ADS)

    Mo, D.; Liu, J. D.; Duan, J. L.; Yao, H. J.; Latif, H.; Cao, D. L.; Chen, Y. H.; Zhang, S. X.; Zhai, P. F.; Liu, J.

    2014-08-01

    A method for the fabrication of different pore shapes in polyethylene terephthalate (PET)-based track etched membranes (TEMs) is reported. A multi-step etching technique involving etchant variation and track annealing was applied to fabricate different pore shapes in PET membranes. PET foils of 12-μm thickness were irradiated with Bi ions (kinetic energy 9.5 MeV/u, fluence 106 ions/cm2) at the Heavy Ion Research Facility (HIRFL, Lanzhou). The cross-sections of fundamental pore shapes (cylinder, cone, and double cone) were analyzed. Funnel-shaped and pencil-shaped pores were obtained using a two-step etching process. Track annealing was carried out in air at 180 °C for 120 min. After track annealing, the selectivity of the etching process decreased, which resulted in isotropic etching in subsequent etching steps. Rounded cylinder and rounded cone shapes were obtained by introducing a track-annealing step in the etching process. Cup and spherical funnel-shaped pores were fabricated using a three- and four-step etching process, respectively. The described multi-step etching technique provides a controllable method to fabricate new pore shapes in TEMs. Introduction of a variety of pore shapes may improve the separation properties of TEMs and enrich the series of TEM products.

  13. Grouped and Multistep Nanoheteroepitaxy: Toward High-Quality GaN on Quasi-Periodic Nano-Mask.

    PubMed

    Feng, Xiaohui; Yu, Tongjun; Wei, Yang; Ji, Cheng; Cheng, Yutian; Zong, Hua; Wang, Kun; Yang, Zhijian; Kang, Xiangning; Zhang, Guoyi; Fan, Shoushan

    2016-07-20

    A novel nanoheteroepitaxy method, namely, the grouped and multistep nanoheteroepitaxy (GM-NHE), is proposed to attain a high-quality gallium nitride (GaN) epilayer by metal-organic vapor phase epitaxy. This method combines the effects of sub-100 nm nucleation and multistep lateral growth by using a low-cost but unique carbon nanotube mask, which consists of nanoscale growth windows with a quasi-periodic 2D fill factor. It is found that GM-NHE can facilely reduce threading dislocation density (TDD) and modulate residual stress on foreign substrate without any regrowth. As a result, high-quality GaN epilayer is produced with homogeneously low TDD of 4.51 × 10(7) cm(-2) and 2D-modulated stress, and the performance of the subsequent 410 nm near-ultraviolet light-emitting diode is greatly boosted. In this way, with the facile fabrication of nanomask and the one-off epitaxy procedure, GaN epilayer is prominently improved with the assistance of nanotechnology, which demonstrates great application potential for high-efficiency TDD-sensitive optoelectronic and electronic devices.

  14. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    PubMed

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Multistep metal insulator transition in VO{sub 2} nanowires on Al{sub 2}O{sub 3} (0001) substrates

    SciTech Connect

    Takami, Hidefumi; Kanki, Teruo E-mail: h-tanaka@sanken.osaka-u.ac.jp; Tanaka, Hidekazu E-mail: h-tanaka@sanken.osaka-u.ac.jp

    2014-01-13

    We observed a temperature- and voltage-induced multistep metal-insulator transition (MIT) in vanadium dioxide nanowires fabricated on Al{sub 2}O{sub 3} (0001) substrates. Nanowires with a width of 200 nm showed a multistep MIT that exhibited a resistivity change of nearly two orders of magnitude in a 0.5 K temperature step. These multistep resistivity jumps can be understood as a transition of a single domain, whose size is estimated to be around 50–70 nm from numerical calculation. We found that the temperature-induced isotropic conductive behavior of the nanowires becomes similar to the voltage-induced anisotropic one as their width decreases.

  16. Comparison of GenomEra C. difficile and Xpert C. difficile as confirmatory tests in a multistep algorithm for diagnosis of Clostridium difficile infection.

    PubMed

    Alcalá, Luis; Reigadas, Elena; Marín, Mercedes; Fernández-Chico, Antonia; Catalán, Pilar; Bouza, Emilio

    2015-01-01

    We compared two multistep diagnostic algorithms based on C. Diff Quik Chek Complete and, as confirmatory tests, GenomEra C. difficile and Xpert C. difficile. The sensitivity, specificity, positive predictive value, and negative predictive value were 87.2%, 99.7%, 97.1%, and 98.3%, respectively, for the GenomEra-based algorithm and 89.7%, 99.4%, 95.5%, and 98.6%, respectively, for the Xpert-based algorithm. GenomEra represents an alternative to Xpert as a confirmatory test of a multistep algorithm for Clostridium difficile infection (CDI) diagnosis.

  17. Automated optical assembly

    NASA Astrophysics Data System (ADS)

    Bala, John L.

    1995-08-01

    Automation and polymer science represent fundamental new technologies which can be directed toward realizing the goal of establishing a domestic, world-class, commercial optics business. Use of innovative optical designs using precision polymer optics will enable the US to play a vital role in the next generation of commercial optical products. The increased cost savings inherent in the utilization of optical-grade polymers outweighs almost every advantage of using glass for high volume situations. Optical designers must gain experience with combined refractive/diffractive designs and broaden their knowledge base regarding polymer technology beyond a cursory intellectual exercise. Implementation of a fully automated assembly system, combined with utilization of polymer optics, constitutes the type of integrated manufacturing process which will enable the US to successfully compete with the low-cost labor employed in the Far East, as well as to produce an equivalent product.

  18. Automated macromolecular crystallization screening

    DOEpatents

    Segelke, Brent W.; Rupp, Bernhard; Krupka, Heike I.

    2005-03-01

    An automated macromolecular crystallization screening system wherein a multiplicity of reagent mixes are produced. A multiplicity of analysis plates is produced utilizing the reagent mixes combined with a sample. The analysis plates are incubated to promote growth of crystals. Images of the crystals are made. The images are analyzed with regard to suitability of the crystals for analysis by x-ray crystallography. A design of reagent mixes is produced based upon the expected suitability of the crystals for analysis by x-ray crystallography. A second multiplicity of mixes of the reagent components is produced utilizing the design and a second multiplicity of reagent mixes is used for a second round of automated macromolecular crystallization screening. In one embodiment the multiplicity of reagent mixes are produced by a random selection of reagent components.

  19. The automated command transmission

    NASA Astrophysics Data System (ADS)

    Inoue, Y.; Satoh, S.

    A technique for automated command transmission (ACT) to GEO-stationed satellites is presented. The system is intended for easing the command center workload. The ACT system determines the relation of the commands to on-board units, connects the telemetry with on-board units, defines the control path on the spacecraft, identifies the correspondence of back-up units to primary units, and ascertains sunlight or eclipse conditions. The system also has the address of satellite and command decoders, the ID and content for the mission command sequence, group and inhibit codes, a listing of all available commands, and restricts the data to a command sequence. Telemetry supplies data for automated problem correction. All other missions operations are terminated during system recovery data processing after a crash. The ACT system is intended for use with the GMS spacecraft.

  20. Automated gas chromatography

    DOEpatents

    Mowry, C.D.; Blair, D.S.; Rodacy, P.J.; Reber, S.D.

    1999-07-13

    An apparatus and process for the continuous, near real-time monitoring of low-level concentrations of organic compounds in a liquid, and, more particularly, a water stream. A small liquid volume of flow from a liquid process stream containing organic compounds is diverted by an automated process to a heated vaporization capillary where the liquid volume is vaporized to a gas that flows to an automated gas chromatograph separation column to chromatographically separate the organic compounds. Organic compounds are detected and the information transmitted to a control system for use in process control. Concentrations of organic compounds less than one part per million are detected in less than one minute. 7 figs.

  1. Automated Pollution Control

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Patterned after the Cassini Resource Exchange (CRE), Sholtz and Associates established the Automated Credit Exchange (ACE), an Internet-based concept that automates the auctioning of "pollution credits" in Southern California. An early challenge of the Jet Propulsion Laboratory's Cassini mission was allocating the spacecraft's resources. To support the decision-making process, the CRE was developed. The system removes the need for the science instrument manager to know the individual instruments' requirements for the spacecraft resources. Instead, by utilizing principles of exchange, the CRE induces the instrument teams to reveal their requirements. In doing so, they arrive at an efficient allocation of spacecraft resources by trading among themselves. A Southern California RECLAIM air pollution credit trading market has been set up using same bartering methods utilized in the Cassini mission in order to help companies keep pollution and costs down.

  2. Automated assembly in space

    NASA Technical Reports Server (NTRS)

    Srivastava, Sandanand; Dwivedi, Suren N.; Soon, Toh Teck; Bandi, Reddy; Banerjee, Soumen; Hughes, Cecilia

    1989-01-01

    The installation of robots and their use of assembly in space will create an exciting and promising future for the U.S. Space Program. The concept of assembly in space is very complicated and error prone and it is not possible unless the various parts and modules are suitably designed for automation. Certain guidelines are developed for part designing and for an easy precision assembly. Major design problems associated with automated assembly are considered and solutions to resolve these problems are evaluated in the guidelines format. Methods for gripping and methods for part feeding are developed with regard to the absence of gravity in space. The guidelines for part orientation, adjustments, compliances and various assembly construction are discussed. Design modifications of various fasteners and fastening methods are also investigated.

  3. Terminal automation system maintenance

    SciTech Connect

    Coffelt, D.; Hewitt, J.

    1997-01-01

    Nothing has improved petroleum product loading in recent years more than terminal automation systems. The presence of terminal automation systems (TAS) at loading racks has increased operational efficiency and safety and enhanced their accounting and management capabilities. However, like all finite systems, they occasionally malfunction or fail. Proper servicing and maintenance can minimize this. And in the unlikely event a TAS breakdown does occur, prompt and effective troubleshooting can reduce its impact on terminal productivity. To accommodate around-the-clock loading at racks, increasingly unattended by terminal personnel, TAS maintenance, servicing and troubleshooting has become increasingly demanding. It has also become increasingly important. After 15 years of trial and error at petroleum and petrochemical storage and transfer terminals, a number of successful troubleshooting programs have been developed. These include 24-hour {open_quotes}help hotlines,{close_quotes} internal (terminal company) and external (supplier) support staff, and {open_quotes}layered{close_quotes} support. These programs are described.

  4. Automated campaign system

    NASA Astrophysics Data System (ADS)

    Vondran, Gary; Chao, Hui; Lin, Xiaofan; Beyer, Dirk; Joshi, Parag; Atkins, Brian; Obrador, Pere

    2006-02-01

    To run a targeted campaign involves coordination and management across numerous organizations and complex process flows. Everything from market analytics on customer databases, acquiring content and images, composing the materials, meeting the sponsoring enterprise brand standards, driving through production and fulfillment, and evaluating results; all processes are currently performed by experienced highly trained staff. Presented is a developed solution that not only brings together technologies that automate each process, but also automates the entire flow so that a novice user could easily run a successful campaign from their desktop. This paper presents the technologies, structure, and process flows used to bring this system together. Highlighted will be how the complexity of running a targeted campaign is hidden from the user through technologies, all while providing the benefits of a professionally managed campaign.

  5. Automated chemiluminescence immunoassay measurements

    NASA Astrophysics Data System (ADS)

    Khalil, Omar S.; Mattingly, G. P.; Genger, K.; Mackowiak, J.; Butler, J.; Pepe, C.; Zurek, T. F.; Abunimeh, N.

    1993-06-01

    Chemiluminescence (CL) detection offers potential for high sensitivity immunoassays (CLIAs). Several approaches were attempted to automate CL measurements. Those include the use of photographic film, clear microtitration plates, and magnetic separation. We describe a photon counting detection apparatus that performs (CLIA) measurements. The CL detector moves toward a disposable reaction vessel to create a light-tight seal and then triggers and integrates a CL signal. The capture uses antibody coated polystyrene microparticles. A porous matrix, which is a part of a disposable reaction tray, entraps the microparticle-captured reaction product. The CL signal emanated off the immune complex immobilized by the porous matrix is detected. The detection system is a part of a fully automated immunoassay analyzer. Methods of achieving high sensitivities are discussed.

  6. Automated Chromosome Breakage Assessment

    NASA Technical Reports Server (NTRS)

    Castleman, Kenneth

    1985-01-01

    An automated karyotyping machine was built at JPL in 1972. It does computerized karyotyping, but it has some hardware limitations. The image processing hardware that was available at a reasonable price in 1972 was marginal, at best, for this job. In the meantime, NASA has developed an interest in longer term spaceflights and an interest in using chromosome breakage studies as a dosimeter for radiation or perhaps other damage that might occur to the tissues. This uses circulating lymphocytes as a physiological dosimeter looking for chromosome breakage on long-term spaceflights. For that reason, we have reactivated the automated karyotyping work at JPL. An update on that work, and a description of where it appears to be headed is presented.

  7. Automated Chromosome Breakage Assessment

    NASA Technical Reports Server (NTRS)

    Castleman, Kenneth

    1985-01-01

    An automated karyotyping machine was built at JPL in 1972. It does computerized karyotyping, but it has some hardware limitations. The image processing hardware that was available at a reasonable price in 1972 was marginal, at best, for this job. In the meantime, NASA has developed an interest in longer term spaceflights and an interest in using chromosome breakage studies as a dosimeter for radiation or perhaps other damage that might occur to the tissues. This uses circulating lymphocytes as a physiological dosimeter looking for chromosome breakage on long-term spaceflights. For that reason, we have reactivated the automated karyotyping work at JPL. An update on that work, and a description of where it appears to be headed is presented.

  8. The automation of science.

    PubMed

    King, Ross D; Rowland, Jem; Oliver, Stephen G; Young, Michael; Aubrey, Wayne; Byrne, Emma; Liakata, Maria; Markham, Magdalena; Pir, Pinar; Soldatova, Larisa N; Sparkes, Andrew; Whelan, Kenneth E; Clare, Amanda

    2009-04-03

    The basis of science is the hypothetico-deductive method and the recording of experiments in sufficient detail to enable reproducibility. We report the development of Robot Scientist "Adam," which advances the automation of both. Adam has autonomously generated functional genomics hypotheses about the yeast Saccharomyces cerevisiae and experimentally tested these hypotheses by using laboratory automation. We have confirmed Adam's conclusions through manual experiments. To describe Adam's research, we have developed an ontology and logical language. The resulting formalization involves over 10,000 different research units in a nested treelike structure, 10 levels deep, that relates the 6.6 million biomass measurements to their logical description. This formalization describes how a machine contributed to scientific knowledge.

  9. Automated Assembly Center (AAC)

    NASA Technical Reports Server (NTRS)

    Stauffer, Robert J.

    1993-01-01

    The objectives of this project are as follows: to integrate advanced assembly and assembly support technology under a comprehensive architecture; to implement automated assembly technologies in the production of high-visibility DOD weapon systems; and to document the improved cost, quality, and lead time. This will enhance the production of DOD weapon systems by utilizing the latest commercially available technologies combined into a flexible system that will be able to readily incorporate new technologies as they emerge. Automated assembly encompasses the following areas: product data, process planning, information management policies and framework, three schema architecture, open systems communications, intelligent robots, flexible multi-ability end effectors, knowledge-based/expert systems, intelligent workstations, intelligent sensor systems, and PDES/PDDI data standards.

  10. Power subsystem automation study

    NASA Technical Reports Server (NTRS)

    Tietz, J. C.; Sewy, D.; Pickering, C.; Sauers, R.

    1984-01-01

    The purpose of the phase 2 of the power subsystem automation study was to demonstrate the feasibility of using computer software to manage an aspect of the electrical power subsystem on a space station. The state of the art in expert systems software was investigated in this study. This effort resulted in the demonstration of prototype expert system software for managing one aspect of a simulated space station power subsystem.

  11. Automated Microbial Metabolism Laboratory

    NASA Technical Reports Server (NTRS)

    1973-01-01

    Development of the automated microbial metabolism laboratory (AMML) concept is reported. The focus of effort of AMML was on the advanced labeled release experiment. Labeled substrates, inhibitors, and temperatures were investigated to establish a comparative biochemical profile. Profiles at three time intervals on soil and pure cultures of bacteria isolated from soil were prepared to establish a complete library. The development of a strategy for the return of a soil sample from Mars is also reported.

  12. Automated RTOP Management System

    NASA Technical Reports Server (NTRS)

    Hayes, P.

    1984-01-01

    The structure of NASA's Office of Aeronautics and Space Technology electronic information system network from 1983 to 1985 is illustrated. The RTOP automated system takes advantage of existing hardware, software, and expertise, and provides: (1) computerized cover sheet and resources forms; (2) electronic signature and transmission; (3) a data-based information system; (4) graphics; (5) intercenter communications; (6) management information; and (7) text editing. The system is coordinated with Headquarters efforts in codes R,E, and T.

  13. Automated RSO Stability Analysis

    NASA Astrophysics Data System (ADS)

    Johnson, T.

    2016-09-01

    A methodology for assessing the attitude stability of a Resident Space Object (RSO) using visual magnitude data is presented and then scaled to run in an automated fashion across the entire satellite catalog. Results obtained by applying the methodology to the Commercial Space Operations Center (COMSpOC) catalog are presented and summarized, identifying objects that have changed stability. We also examine the timeline for detecting the transition from stable to unstable attitude

  14. Automated Nitrocellulose Analysis

    DTIC Science & Technology

    1978-12-01

    is acceptable. (4) As would be expected from the theory of osmosis , a high saline content in the dialysis recipient stream (countersolution) is of...Block 39, II different from Report; IS. SUPPLEMENTARY NOTES IS. KEY WOROS (Continue on rereri Analysis Automated analysis Dialysis Glyceryl...Technicon AutoAnalyzer, involves aspiration of a stirred nitrocellulose suspension, dialysis against 9 percent saline, and hydrolysis with 5N sodium

  15. Cavendish Balance Automation

    NASA Technical Reports Server (NTRS)

    Thompson, Bryan

    2000-01-01

    This is the final report for a project carried out to modify a manual commercial Cavendish Balance for automated use in cryostat. The scope of this project was to modify an off-the-shelf manually operated Cavendish Balance to allow for automated operation for periods of hours or days in cryostat. The purpose of this modification was to allow the balance to be used in the study of effects of superconducting materials on the local gravitational field strength to determine if the strength of gravitational fields can be reduced. A Cavendish Balance was chosen because it is a fairly simple piece of equipment for measuring gravity, one the least accurately known and least understood physical constants. The principle activities that occurred under this purchase order were: (1) All the components necessary to hold and automate the Cavendish Balance in a cryostat were designed. Engineering drawings were made of custom parts to be fabricated, other off-the-shelf parts were procured; (2) Software was written in LabView to control the automation process via a stepper motor controller and stepper motor, and to collect data from the balance during testing; (3)Software was written to take the data collected from the Cavendish Balance and reduce it to give a value for the gravitational constant; (4) The components of the system were assembled and fitted to a cryostat. Also the LabView hardware including the control computer, stepper motor driver, data collection boards, and necessary cabling were assembled; and (5) The system was operated for a number of periods, data collected, and reduced to give an average value for the gravitational constant.

  16. Automated Cooperative Trajectories

    NASA Technical Reports Server (NTRS)

    Hanson, Curt; Pahle, Joseph; Brown, Nelson

    2015-01-01

    This presentation is an overview of the Automated Cooperative Trajectories project. An introduction to the phenomena of wake vortices is given, along with a summary of past research into the possibility of extracting energy from the wake by flying close parallel trajectories. Challenges and barriers to adoption of civilian automatic wake surfing technology are identified. A hardware-in-the-loop simulation is described that will support future research. Finally, a roadmap for future research and technology transition is proposed.

  17. Algorithms for automated DNA assembly

    PubMed Central

    Densmore, Douglas; Hsiau, Timothy H.-C.; Kittleson, Joshua T.; DeLoache, Will; Batten, Christopher; Anderson, J. Christopher

    2010-01-01

    Generating a defined set of genetic constructs within a large combinatorial space provides a powerful method for engineering novel biological functions. However, the process of assembling more than a few specific DNA sequences can be costly, time consuming and error prone. Even if a correct theoretical construction scheme is developed manually, it is likely to be suboptimal by any number of cost metrics. Modular, robust and formal approaches are needed for exploring these vast design spaces. By automating the design of DNA fabrication schemes using computational algorithms, we can eliminate human error while reducing redundant operations, thus minimizing the time and cost required for conducting biological engineering experiments. Here, we provide algorithms that optimize the simultaneous assembly of a collection of related DNA sequences. We compare our algorithms to an exhaustive search on a small synthetic dataset and our results show that our algorithms can quickly find an optimal solution. Comparison with random search approaches on two real-world datasets show that our algorithms can also quickly find lower-cost solutions for large datasets. PMID:20335162

  18. Automation in biological crystallization.

    PubMed

    Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

    2014-06-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

  19. Automation in biological crystallization

    PubMed Central

    Shaw Stewart, Patrick; Mueller-Dieckmann, Jochen

    2014-01-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given. PMID:24915074

  20. Autonomy, Automation, and Systems

    NASA Astrophysics Data System (ADS)

    Turner, Philip R.

    1987-02-01

    Aerospace industry interest in autonomy and automation, given fresh impetus by the national goal of establishing a Space Station, is becoming a major item of research and technology development. The promise of new technology arising from research in Artificial Intelligence (AI) has focused much attention on its potential in autonomy and automation. These technologies can improve performance in autonomous control functions that involve planning, scheduling, and fault diagnosis of complex systems. There are, however, many aspects of system and subsystem design in an autonomous system that impact AI applications, but do not directly involve AI technology. Development of a system control architecture, establishment of an operating system within the design, providing command and sensory data collection features appropriate to automated operation, and the use of design analysis tools to support system engineering are specific examples of major design issues. Aspects such as these must also receive attention and technology development support if we are to implement complex autonomous systems within the realistic limitations of mass, power, cost, and available flight-qualified technology that are all-important to a flight project.

  1. Automating existing stations

    SciTech Connect

    Little, J.E.

    1986-09-01

    The task was to automate 20 major compressor stations along ANR Pipeline Co.'s Southeastern and Southwestern pipelines in as many months. Meeting this schedule required standardized hardware and software design. Working with Bristol Babcock Co., ANR came up with an off-the-shelf station automation package suitable for a variety of compressor stations. The project involved 148 engines with 488,880-hp in the 20 stations. ANR Pipeline developed software for these engines and compressors, including horsepower prediction and efficiency. The system places processors ''intelligence'' at each station and engine to monitor and control operations. The station processor receives commands from the company's gas dispatch center at Detroit and informs dispatchers of alarms, conditions, and decision it makes. The automation system is controlled by the Detroit center through a central communications network. Operating orders from the center are sent to the station processor, which obeys orders using the most efficient means of operation at the station's disposal. In a malfunction, a control and communications backup system takes over. Commands and information are directly transmitted between the center and the individual compressor stations. Stations receive their orders based on throughput, with suction and discharge pressure overrides. Additionally, a discharge temperature override protects pipeline coatings.

  2. Automation of optical tweezers

    NASA Astrophysics Data System (ADS)

    Hsieh, Tseng-Ming; Chang, Bo-Jui; Hsu, Long

    2000-07-01

    Optical tweezers is a newly developed instrument, which makes possible the manipulation of micro-optical particles under a microscope. In this paper, we present the automation of an optical tweezers which consists of a modified optical tweezers, equipped with two motorized actuators to deflect a 1 W argon laser beam, and a computer control system including a joystick. The trapping of a single bead and a group of lactoacidofilus was shown, separately. With the aid of the joystick and two auxiliary cursers superimposed on the real-time image of a trapped bead, we demonstrated the simple and convenient operation of the automated optical tweezers. By steering the joystick and then pressing a button on it, we assign a new location for the trapped bead to move to. The increment of the motion 0.04 (mu) m for a 20X objective, is negligible. With a fast computer for image processing, the manipulation of the trapped bead is smooth and accurate. The automation of the optical tweezers is also programmable. This technique may be applied to accelerate the DNA hybridization in a gene chip. The combination of the modified optical tweezers with the computer control system provides a tool for precise manipulation of micro particles in many scientific fields.

  3. Automation model of sewerage rehabilitation planning.

    PubMed

    Yang, M D; Su, T C

    2006-01-01

    The major steps of sewerage rehabilitation include inspection of sewerage, assessment of structural conditions, computation of structural condition grades, and determination of rehabilitation methods and materials. Conventionally, sewerage rehabilitation planning relies on experts with professional background that is tedious and time-consuming. This paper proposes an automation model of planning optimal sewerage rehabilitation strategies for the sewer system by integrating image process, clustering technology, optimization, and visualization display. Firstly, image processing techniques, such as wavelet transformation and co-occurrence features extraction, were employed to extract various characteristics of structural failures from CCTV inspection images. Secondly, a classification neural network was established to automatically interpret the structural conditions by comparing the extracted features with the typical failures in a databank. Then, to achieve optimal rehabilitation efficiency, a genetic algorithm was used to determine appropriate rehabilitation methods and substitution materials for the pipe sections with a risk of mal-function and even collapse. Finally, the result from the automation model can be visualized in a geographic information system in which essential information of the sewer system and sewerage rehabilitation plans are graphically displayed. For demonstration, the automation model of optimal sewerage rehabilitation planning was applied to a sewer system in east Taichung, Chinese Taiwan.

  4. Genetic and Developmental Basis of Cardiovascular Malformations

    PubMed Central

    Azhar, Mohamad; Ware, Stephanie M.

    2015-01-01

    Cardiovascular malformations (CVMs) are the most common birth defect, occurring in 1–5% of all live births. Genetic, epigenetic, and environmental factors all influence the development of CVMs, and an improved understanding of causation of CVMs is a prerequisite for prevention. Cardiac development is a complex, multi-step process of morphogenesis that is under genetic regulation. Multiple developmental pathways act independently or in combination to effect proper cardiac lineage specification, differentiation, and structure. Because of this complexity, there are numerous potential mechanisms by which genetic variation can impact both fetal cardiac development and latent cardiac disease. Although the genetic contribution to CVMs is well recognized, the genetic causes of human CVMs are still identified relatively infrequently. Mouse models are important tools to investigate the molecular mechanisms underpinning cardiac development as well as the complex genetics that characterize human CVMs. In this review we provide an overview of the key genetic concepts characterizing human CVMs, review their developmental basis, and provide examples to illustrate the critical developmental and genetic concepts underlying the pathogenesis of CVMs. PMID:26876120

  5. AUTOMATED INADVERTENT INTRUDER APPLICATION

    SciTech Connect

    Koffman, L; Patricia Lee, P; Jim Cook, J; Elmer Wilhite, E

    2007-05-29

    The Environmental Analysis and Performance Modeling group of Savannah River National Laboratory (SRNL) conducts performance assessments of the Savannah River Site (SRS) low-level waste facilities to meet the requirements of DOE Order 435.1. These performance assessments, which result in limits on the amounts of radiological substances that can be placed in the waste disposal facilities, consider numerous potential exposure pathways that could occur in the future. One set of exposure scenarios, known as inadvertent intruder analysis, considers the impact on hypothetical individuals who are assumed to inadvertently intrude onto the waste disposal site. Inadvertent intruder analysis considers three distinct scenarios for exposure referred to as the agriculture scenario, the resident scenario, and the post-drilling scenario. Each of these scenarios has specific exposure pathways that contribute to the overall dose for the scenario. For the inadvertent intruder analysis, the calculation of dose for the exposure pathways is a relatively straightforward algebraic calculation that utilizes dose conversion factors. Prior to 2004, these calculations were performed using an Excel spreadsheet. However, design checks of the spreadsheet calculations revealed that errors could be introduced inadvertently when copying spreadsheet formulas cell by cell and finding these errors was tedious and time consuming. This weakness led to the specification of functional requirements to create a software application that would automate the calculations for inadvertent intruder analysis using a controlled source of input parameters. This software application, named the Automated Inadvertent Intruder Application, has undergone rigorous testing of the internal calculations and meets software QA requirements. The Automated Inadvertent Intruder Application was intended to replace the previous spreadsheet analyses with an automated application that was verified to produce the same calculations and

  6. Effects of Stroke on Ipsilesional End-Effector Kinematics in a Multi-Step Activity of Daily Living

    PubMed Central

    Gulde, Philipp; Hughes, Charmayne Mary Lee; Hermsdörfer, Joachim

    2017-01-01

    Background: Stroke frequently impairs activities of daily living (ADL) and deteriorates the function of the contra- as well as the ipsilesional limbs. In order to analyze alterations of higher motor control unaffected by paresis or sensory loss, the kinematics of ipsilesional upper limb movements in patients with stroke has previously been analyzed during prehensile movements and simple tool use actions. By contrast, motion recording of multi-step ADL is rare and patient-control comparisons for movement kinematics are largely lacking. Especially in clinical research, objective quantification of complex externally valid tasks can improve the assessment of neurological impairments. Methods: In this preliminary study we employed three-dimensional motion recording and applied kinematic analysis in a multi-step ADL (tea-making). The trials were examined with respect to errors and sub-action structure, durations, path lengths (PLs), peak velocities, relative activity (RA) and smoothness. In order to check for specific burdens the sub-actions of the task were extracted and compared. To examine the feasibility of the approach, we determined the behavioral and kinematic metrics of the (ipsilesional) unimanual performance of seven chronic stroke patients (64a ± 11a, 3 with right/4 with left brain damage (LBD), 2 with signs of apraxia, variable severity of paresis) and compared the results with data of 14 neurologically healthy age-matched control participants (70a ± 7a). Results: T-tests revealed that while the quantity and structure of sub-actions of the task were similar. The analysis of end-effector kinematics was able to detect clear group differences in the associated parameters. Specifically, trial duration (TD) was increased (Cohen’s d = 1.77); the RA (Cohen’s d = 1.72) and the parameters of peak velocities (Cohen’s d = 1.49/1.97) were decreased in the patient group. Analysis of the task’s sub-actions repeated measures analysis of variance (rmANOVA) revealed

  7. Genetic Counseling

    MedlinePlus

    ... Home > Pregnancy > Before or between pregnancies > Genetic counseling Genetic counseling E-mail to a friend Please fill ... a genetic counselor in your area. What is genetic counseling? Genetic counseling helps you understand how genes , ...

  8. Predictions for rapid methods and automation in food microbiology.

    PubMed

    Fung, Daniel Y C

    2002-01-01

    A discussion is presented on the present status of rapid methods and automation in microbiology. Predictions are also presented for development in the following areas: viable cell counts; real-time monitoring of hygiene; polymerase chain reaction, ribotyping, and genetic tests in food laboratories; automated enzyme-linked immunosorbent assay and immunotests; rapid dipstick technology; biosensors for Hazard Analysis Critical Control Point programs; instant detection of target pathogens by computer-generated matrix; effective separation and concentration for rapid identification of target cells; microbiological alert systems in food packages; and rapid alert kits for detecting pathogens at home.

  9. Automated Proactive Fault Isolation: A Key to Automated Commissioning

    SciTech Connect

    Katipamula, Srinivas; Brambley, Michael R.

    2007-07-31

    In this paper, we present a generic model for automated continuous commissioing and then delve in detail into one of the processes, proactive testing for fault isolation, which is key to automating commissioning. The automated commissioining process uses passive observation-based fault detction and diagnostic techniques, followed by automated proactive testing for fault isolation, automated fault evaluation, and automated reconfiguration of controls together to continuously keep equipment controlled and running as intended. Only when hard failures occur or a physical replacement is required does the process require human intervention, and then sufficient information is provided by the automated commissioning system to target manual maintenance where it is needed. We then focus on fault isolation by presenting detailed logic that can be used to automatically isolate faults in valves, a common component in HVAC systems, as an example of how automated proactive fault isolation can be accomplished. We conclude the paper with a discussion of how this approach to isolating faults can be applied to other common HVAC components and their automated commmissioning and a summary of key conclusions of the paper.

  10. Automated genotyping of dinucleotide repeat markers

    SciTech Connect

    Perlin, M.W.; Hoffman, E.P. |

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  11. PaR-PaR laboratory automation platform.

    PubMed

    Linshiz, Gregory; Stawski, Nina; Poust, Sean; Bi, Changhao; Keasling, Jay D; Hillson, Nathan J

    2013-05-17

    Labor-intensive multistep biological tasks, such as the construction and cloning of DNA molecules, are prime candidates for laboratory automation. Flexible and biology-friendly operation of robotic equipment is key to its successful integration in biological laboratories, and the efforts required to operate a robot must be much smaller than the alternative manual lab work. To achieve these goals, a simple high-level biology-friendly robot programming language is needed. We have developed and experimentally validated such a language: Programming a Robot (PaR-PaR). The syntax and compiler for the language are based on computer science principles and a deep understanding of biological workflows. PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour. Adoption of PaR-PaR as a standard cross-platform language would enable hand-written or software-generated robotic protocols to be shared across laboratories.

  12. PaR-PaR Laboratory Automation Platform

    SciTech Connect

    Linshiz, G; Stawski, N; Poust, S; Bi, CH; Keasling, JD; Hilson, NJ

    2013-05-01

    Labor-intensive multistep biological tasks, such as the construction and cloning of DNA molecules, are prime candidates for laboratory automation. Flexible and biology-friendly operation of robotic equipment is key to its successful integration in biological laboratories, and the efforts required to operate a robot must be much smaller than the alternative manual lab work. To achieve these goals, a simple high-level biology-friendly robot programming language is needed. We have developed and experimentally validated such a language: Programming a Robot (PaR-PaR). The syntax and compiler for the language are based on computer science principles and a deep understanding of biological workflows. PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour. Adoption of PaR-PaR as a standard cross-platform language would enable hand-written or software-generated robotic protocols to be shared across laboratories.

  13. Automation in organizations: Eternal conflict

    NASA Technical Reports Server (NTRS)

    Dieterly, D. L.

    1981-01-01

    Some ideas on and insights into the problems associated with automation in organizations are presented with emphasis on the concept of automation, its relationship to the individual, and its impact on system performance. An analogy is drawn, based on an American folk hero, to emphasize the extent of the problems encountered when dealing with automation within an organization. A model is proposed to focus attention on a set of appropriate dimensions. The function allocation process becomes a prominent aspect of the model. The current state of automation research is mentioned in relation to the ideas introduced. Proposed directions for an improved understanding of automation's effect on the individual's efficiency are discussed. The importance of understanding the individual's perception of the system in terms of the degree of automation is highlighted.

  14. Teaching multi-step requesting and social communication to two children with autism spectrum disorders with three AAC options.

    PubMed

    van der Meer, Larah; Kagohara, Debora; Roche, Laura; Sutherland, Dean; Balandin, Susan; Green, Vanessa A; O'Reilly, Mark F; Lancioni, Giulio E; Marschik, Peter B; Sigafoos, Jeff

    2013-09-01

    The present study involved comparing the acquisition of multi-step requesting and social communication across three AAC options: manual signing (MS), picture exchange (PE), and speech-generating devices (SGDs). Preference for each option was also assessed. The participants were two children with autism spectrum disorders (ASD) who had previously been taught to use each option to request preferred items. Intervention was implemented in an alternating-treatments design. During baseline, participants demonstrated low levels of correct communicative responding. With intervention, both participants learned the target responses (two- and three-step requesting responses, greetings, answering questions, and social etiquette responses) to varying levels of proficiency with each communication option. One participant demonstrated a preference for using the SGD and the other preferred PE. The importance of examining preferences for using one AAC option over others is discussed.

  15. Texture and anisotropy of yield strength in multistep isothermally forged Mg-5.8Zn-0.65Zr alloy

    NASA Astrophysics Data System (ADS)

    Nugmanov, D. R.; Sitdikov, O. Sh; Markushev, M. V.

    2015-04-01

    The effect of multistep isothermal forging (MIF) on microstructure, texture and anisotropy of ambient temperature yield strength of MA14 (Mg-5.8Mg-0.65Zr (%, wt)) magnesium alloy hot-pressed rod was analyzed. It has been found that the initial axial texture is quite stable under 1st MIF step up to strain e∼4.2 at 400°C and has been gradually transformed into much weaker single-peak one at further processing at 300 and 200°C to total strain of 10.2. Such texture changes were accompanied by strong grain refinement, along with significant reduction of the alloy strength anisotropy.

  16. Deterministic multi-step rotation of magnetic single-domain state in Nickel nanodisks using multiferroic magnetoelastic coupling

    NASA Astrophysics Data System (ADS)

    Sohn, Hyunmin; Liang, Cheng-yen; Nowakowski, Mark E.; Hwang, Yongha; Han, Seungoh; Bokor, Jeffrey; Carman, Gregory P.; Candler, Robert N.

    2017-10-01

    We demonstrate deterministic multi-step rotation of a magnetic single-domain (SD) state in Nickel nanodisks using the multiferroic magnetoelastic effect. Ferromagnetic Nickel nanodisks are fabricated on a piezoelectric Lead Zirconate Titanate (PZT) substrate, surrounded by patterned electrodes. With the application of a voltage between opposing electrode pairs, we generate anisotropic in-plane strains that reshape the magnetic energy landscape of the Nickel disks, reorienting magnetization toward a new easy axis. By applying a series of voltages sequentially to adjacent electrode pairs, circulating in-plane anisotropic strains are applied to the Nickel disks, deterministically rotating a SD state in the Nickel disks by increments of 45°. The rotation of the SD state is numerically predicted by a fully-coupled micromagnetic/elastodynamic finite element analysis (FEA) model, and the predictions are experimentally verified with magnetic force microscopy (MFM). This experimental result will provide a new pathway to develop energy efficient magnetic manipulation techniques at the nanoscale.

  17. Strong textured SmCo5 nanoflakes with ultrahigh coercivity prepared by multistep (three steps) surfactant-assisted ball milling.

    PubMed

    Zuo, Wen-Liang; Zhao, Xin; Xiong, Jie-Fu; Zhang, Ming; Zhao, Tong-Yun; Hu, Feng-Xia; Sun, Ji-Rong; Shen, Bao-Gen

    2015-08-14

    The high coercivity of 26.2 kOe for SmCo5 nanoflakes are obtained by multistep (three steps) surfactant-assisted ball milling. The magnetic properties, phase structure and morphology are studied by VSM, XRD and SEM, respectively. The results demonstrate that the three step ball-milling can keep more complete crystallinity (relatively less defects) during the process of milling compared with one step high energy ball-milling, which enhances the texture degree and coercivity. In addition, the mechanism of coercivity are also studied by the temperature dependence of demagnetization curves for aligned SmCo5 nanoflakes/resin composite, the result indicates that the magnetization reversal could be controlled by co-existed mechanisms of pinning and nucleation.

  18. Discovery of novel, non-acidic mPGES-1 inhibitors by virtual screening with a multistep protocol

    PubMed Central

    Noha, Stefan M.; Fischer, Katrin; Koeberle, Andreas; Garscha, Ulrike; Werz, Oliver; Schuster, Daniela

    2015-01-01

    Microsomal prostaglandin E2 synthase-1 (mPGES-1) inhibitors are considered as potential therapeutic agents for the treatment of inflammatory pain and certain types of cancer. So far, several series of acidic as well as non-acidic inhibitors of mPGES-1 have been discovered. Acidic inhibitors, however, may have issues, such as loss of potency in human whole blood and in vivo, stressing the importance of the design and identification of novel, non-acidic chemical scaffolds of mPGES-1 inhibitors. Using a multistep virtual screening protocol, the Vitas-M compound library (∼1.3 million entries) was filtered and 16 predicted compounds were experimentally evaluated in a biological assay in vitro. This approach yielded two molecules active in the low micromolar range (IC50 values: 4.5 and 3.8 μM, respectively). PMID:26088337

  19. Multistep continuous-flow synthesis in medicinal chemistry: discovery and preliminary structure-activity relationships of CCR8 ligands.

    PubMed

    Petersen, Trine P; Mirsharghi, Sahar; Rummel, Pia C; Thiele, Stefanie; Rosenkilde, Mette M; Ritzén, Andreas; Ulven, Trond

    2013-07-08

    A three-step continuous-flow synthesis system and its application to the assembly of a new series of chemokine receptor ligands directly from commercial building blocks is reported. No scavenger columns or solvent switches are necessary to recover the desired test compounds, which were obtained in overall yields of 49-94%. The system is modular and flexible, and the individual steps of the sequence can be interchanged with similar outcome, extending the scope of the chemistry. Biological evaluation confirmed activity on the chemokine CCR8 receptor and provided initial structure-activity-relationship (SAR) information for this new ligand series, with the most potent member displaying full agonist activity with single-digit nanomolar potency. To the best of our knowledge, this represents the first published example of efficient use of multistep flow synthesis combined with biological testing and SAR studies in medicinal chemistry. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. A versatile valving toolkit for automating fluidic operations in paper microfluidic devices

    PubMed Central

    Toley, Bhushan J.; Wang, Jessica A.; Gupta, Mayuri; Buser, Joshua R.; Lafleur, Lisa K.; Lutz, Barry R.; Fu, Elain; Yager, Paul

    2015-01-01

    Failure to utilize valving and automation techniques has restricted the complexity of fluidic operations that can be performed in paper microfluidic devices. We developed a toolkit of paper microfluidic valves and methods for automatic valve actuation using movable paper strips and fluid-triggered expanding elements. To the best of our knowledge, this is the first functional demonstration of this valving strategy in paper microfluidics. After introduction of fluids on devices, valves can actuate automatically a) after a certain period of time, or b) after the passage of a certain volume of fluid. Timing of valve actuation can be tuned with greater than 8.5% accuracy by changing lengths of timing wicks, and we present timed on-valves, off-valves, and diversion (channel-switching) valves. The actuators require ~30 μl fluid to actuate and the time required to switch from one state to another ranges from ~5 s for short to ~50s for longer wicks. For volume-metered actuation, the size of a metering pad can be adjusted to tune actuation volume, and we present two methods – both methods can achieve greater than 9% accuracy. Finally, we demonstrate the use of these valves in a device that conducts a multi-step assay for the detection of the malaria protein PfHRP2. Although slightly more complex than devices that do not have moving parts, this valving and automation toolkit considerably expands the capabilities of paper microfluidic devices. Components of this toolkit can be used to conduct arbitrarily complex, multi-step fluidic operations on paper-based devices, as demonstrated in the malaria assay device. PMID:25606810

  1. 77 FR 48527 - National Customs Automation Program (NCAP) Test Concerning Automated Commercial Environment (ACE...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-14

    ... Automated Commercial Environment (ACE) Simplified Entry: Modification of Participant Selection Criteria and... (NCAP) test concerning the simplified entry functionality in the Automated Commercial Environment (ACE...) National Customs Automation Program (NCAP) test concerning Automated Commercial Environment (ACE...

  2. A multistep voriconazole-related phototoxic pathway may lead to skin carcinoma: results from a French nationwide study.

    PubMed

    Epaulard, Olivier; Villier, Céline; Ravaud, Philippe; Chosidow, Olivier; Blanche, Stéphane; Mamzer-Bruneel, Marie-France; Thiébaut, Anne; Leccia, Marie-Thérèse; Lortholary, Olivier

    2013-12-01

    Voriconazole long-term therapy is suspected to induce cutaneous squamous cell carcinoma (SCC), as suggested by 18 case reports worldwide and 3 retrospective studies. To better characterize the natural history of these potentially voriconazole-associated tumors, a nationwide call for notification of skin cancers and other skin lesions observed between 2002 and 2012 in patients treated by voriconazole was launched in France. A multidisciplinary committee evaluated voriconazole involvement in each case. Nineteen SCCs were reported. The committee determined the likelihood of voriconazole involvement to be high in 15 cases, intermediate in 2, and low in 2. In the 17 patients with high/intermediate likelihood of voriconazole involvement, the mean time between voriconazole initiation and SCC diagnosis was 39 ± 18 months (range, 28-84 months), and was shorter in transplant recipients (35 vs 45 months, P < .05). Cumulative mean duration of voriconazole therapy at SCC diagnosis was 35 months (range, 7-63 months). A multistep process was noted in 14 of 17 patients: acute phototoxicity during the first year of voriconazole therapy (mean time, 6 months [range, 0-18 months]), actinic keratosis (AK) of the same sun-exposed skin area in the second/third year (mean, 30 months [range, 11-57 months]), followed by SCC during the third year or later. Five cases of AK without SCC and 37 cases of other skin lesions were also reported. Our results suggest that long-term voriconazole prescription may be associated with a multistep phototoxic process involving acute skin lesions followed by AK then by SCC. Discontinuation of voriconazole should be strongly considered in patients experiencing chronic phototoxicity.

  3. World-wide distribution automation systems

    SciTech Connect

    Devaney, T.M.

    1994-12-31

    A worldwide power distribution automation system is outlined. Distribution automation is defined and the status of utility automation is discussed. Other topics discussed include a distribution management system, substation feeder, and customer functions, potential benefits, automation costs, planning and engineering considerations, automation trends, databases, system operation, computer modeling of system, and distribution management systems.

  4. The independent use of self-instructions for the acquisition of untrained multi-step tasks for individuals with an intellectual disability: A review of the literature.

    PubMed

    Smith, Katie A; Shepley, Sally B; Alexander, Jennifer L; Ayres, Kevin M

    2015-05-01

    Systematic instruction on multi-step tasks (e.g., cooking, vocational skills, personal hygiene) is common for individuals with an intellectual disability. Unfortunately, when individuals with disabilities turn 22-years-old, they no longer receive services in the public school system in most states and systematic instruction often ends (Bouck, 2012). Rather than focusing instructional time on teacher-delivered training on the acquisition of specific multi-step tasks, teaching individuals with disabilities a pivotal skill, such as using self-instructional strategies, may be a more meaningful use of time. By learning self-instruction strategies that focus on generalization, individuals with disabilities can continue acquiring novel multi-step tasks in post-secondary settings and remediate skills that are lost over time. This review synthesizes the past 30 years of research related to generalized self-instruction to learn multi-step tasks, provides information about the types of self-instructional materials used, the ways in which participants received training to use them, and concludes with implications for practitioners and recommendations for future research. Published by Elsevier Ltd.

  5. Continuous Video Modeling to Assist with Completion of Multi-Step Home Living Tasks by Young Adults with Moderate Intellectual Disability

    ERIC Educational Resources Information Center

    Mechling, Linda C.; Ayres, Kevin M.; Bryant, Kathryn J.; Foster, Ashley L.

    2014-01-01

    The current study evaluated a relatively new video-based procedure, continuous video modeling (CVM), to teach multi-step cleaning tasks to high school students with moderate intellectual disability. CVM in contrast to video modeling and video prompting allows repetition of the video model (looping) as many times as needed while the user completes…

  6. Facilitating Students' Review of the Chemistry of Nitrogen-Containing Heterocyclic Compounds and Their Characterization through Multistep Synthesis of Thieno[2,3-"b"]Pyridine Derivatives

    ERIC Educational Resources Information Center

    Liu, Hanlin; Zaplishnyy, Vladimir; Mikhaylichenko, Lana

    2016-01-01

    A multistep synthesis of thieno[2,3-"b"]pyridine derivatives is described that is suitable for the upper-level undergraduate organic laboratory. This experiment exposes students to various hands-on experimental techniques as well as methods of product characterization such as IR and [superscript 1]H NMR spectroscopy, and…

  7. Coping Strategies Applied to Comprehend Multistep Arithmetic Word Problems by Students with Above-Average Numeracy Skills and Below-Average Reading Skills

    ERIC Educational Resources Information Center

    Nortvedt, Guri A.

    2011-01-01

    This article discusses how 13-year-old students with above-average numeracy skills and below-average reading skills cope with comprehending word problems. Compared to other students who are proficient in numeracy and are skilled readers, these students are more disadvantaged when solving single-step and multistep arithmetic word problems. The…

  8. Coping Strategies Applied to Comprehend Multistep Arithmetic Word Problems by Students with Above-Average Numeracy Skills and Below-Average Reading Skills

    ERIC Educational Resources Information Center

    Nortvedt, Guri A.

    2011-01-01

    This article discusses how 13-year-old students with above-average numeracy skills and below-average reading skills cope with comprehending word problems. Compared to other students who are proficient in numeracy and are skilled readers, these students are more disadvantaged when solving single-step and multistep arithmetic word problems. The…

  9. Facilitating Students' Review of the Chemistry of Nitrogen-Containing Heterocyclic Compounds and Their Characterization through Multistep Synthesis of Thieno[2,3-"b"]Pyridine Derivatives

    ERIC Educational Resources Information Center

    Liu, Hanlin; Zaplishnyy, Vladimir; Mikhaylichenko, Lana

    2016-01-01

    A multistep synthesis of thieno[2,3-"b"]pyridine derivatives is described that is suitable for the upper-level undergraduate organic laboratory. This experiment exposes students to various hands-on experimental techniques as well as methods of product characterization such as IR and [superscript 1]H NMR spectroscopy, and…

  10. Automating CPM-GOMS

    NASA Technical Reports Server (NTRS)

    John, Bonnie; Vera, Alonso; Matessa, Michael; Freed, Michael; Remington, Roger

    2002-01-01

    CPM-GOMS is a modeling method that combines the task decomposition of a GOMS analysis with a model of human resource usage at the level of cognitive, perceptual, and motor operations. CPM-GOMS models have made accurate predictions about skilled user behavior in routine tasks, but developing such models is tedious and error-prone. We describe a process for automatically generating CPM-GOMS models from a hierarchical task decomposition expressed in a cognitive modeling tool called Apex. Resource scheduling in Apex automates the difficult task of interleaving the cognitive, perceptual, and motor resources underlying common task operators (e.g. mouse move-and-click). Apex's UI automatically generates PERT charts, which allow modelers to visualize a model's complex parallel behavior. Because interleaving and visualization is now automated, it is feasible to construct arbitrarily long sequences of behavior. To demonstrate the process, we present a model of automated teller interactions in Apex and discuss implications for user modeling. available to model human users, the Goals, Operators, Methods, and Selection (GOMS) method [6, 21] has been the most widely used, providing accurate, often zero-parameter, predictions of the routine performance of skilled users in a wide range of procedural tasks [6, 13, 15, 27, 28]. GOMS is meant to model routine behavior. The user is assumed to have methods that apply sequences of operators and to achieve a goal. Selection rules are applied when there is more than one method to achieve a goal. Many routine tasks lend themselves well to such decomposition. Decomposition produces a representation of the task as a set of nested goal states that include an initial state and a final state. The iterative decomposition into goals and nested subgoals can terminate in primitives of any desired granularity, the choice of level of detail dependent on the predictions required. Although GOMS has proven useful in HCI, tools to support the

  11. Automating CPM-GOMS

    NASA Technical Reports Server (NTRS)

    John, Bonnie; Vera, Alonso; Matessa, Michael; Freed, Michael; Remington, Roger

    2002-01-01

    CPM-GOMS is a modeling method that combines the task decomposition of a GOMS analysis with a model of human resource usage at the level of cognitive, perceptual, and motor operations. CPM-GOMS models have made accurate predictions about skilled user behavior in routine tasks, but developing such models is tedious and error-prone. We describe a process for automatically generating CPM-GOMS models from a hierarchical task decomposition expressed in a cognitive modeling tool called Apex. Resource scheduling in Apex automates the difficult task of interleaving the cognitive, perceptual, and motor resources underlying common task operators (e.g. mouse move-and-click). Apex's UI automatically generates PERT charts, which allow modelers to visualize a model's complex parallel behavior. Because interleaving and visualization is now automated, it is feasible to construct arbitrarily long sequences of behavior. To demonstrate the process, we present a model of automated teller interactions in Apex and discuss implications for user modeling. available to model human users, the Goals, Operators, Methods, and Selection (GOMS) method [6, 21] has been the most widely used, providing accurate, often zero-parameter, predictions of the routine performance of skilled users in a wide range of procedural tasks [6, 13, 15, 27, 28]. GOMS is meant to model routine behavior. The user is assumed to have methods that apply sequences of operators and to achieve a goal. Selection rules are applied when there is more than one method to achieve a goal. Many routine tasks lend themselves well to such decomposition. Decomposition produces a representation of the task as a set of nested goal states that include an initial state and a final state. The iterative decomposition into goals and nested subgoals can terminate in primitives of any desired granularity, the choice of level of detail dependent on the predictions required. Although GOMS has proven useful in HCI, tools to support the

  12. Automation for optics manufacturing

    NASA Astrophysics Data System (ADS)

    Pollicove, Harvey M.; Moore, Duncan T.

    1990-11-01

    The optics industry has not followed the lead of the machining and electronics industries in applying advances In computer aided engineering (CAE), computer assisted manufacturing (CAM), automation or quality management techniques. Automationbased on computer integrated manufacturing (CIM) and flexible machining systems (FMS) has been widely implemented In these industries. Optics continues to rely on standalone equipment that preserves the highly skilled, labor intensive optical fabrication systems developed in the 1940's. This paper describes development initiatives at the Center for Optics Manufacturing that will create computer integrated manufacturing technology and support processes for the optical industry.

  13. Automated Propellant Blending

    NASA Technical Reports Server (NTRS)

    Hohmann, Carl W. (Inventor); Harrington, Douglas W. (Inventor); Dutton, Maureen L. (Inventor); Tipton, Billy Charles, Jr. (Inventor); Bacak, James W. (Inventor); Salazar, Frank (Inventor)

    2000-01-01

    An automated propellant blending apparatus and method that uses closely metered addition of countersolvent to a binder solution with propellant particles dispersed therein to precisely control binder precipitation and particle aggregation is discussed. A profile of binder precipitation versus countersolvent-solvent ratio is established empirically and used in a computer algorithm to establish countersolvent addition parameters near the cloud point for controlling the transition of properties of the binder during agglomeration and finishing of the propellant composition particles. The system is remotely operated by computer for safety, reliability and improved product properties, and also increases product output.

  14. [Automated anesthesia record system].

    PubMed

    Zhu, Tao; Liu, Jin

    2005-12-01

    Based on Client/Server architecture, a software of automated anesthesia record system running under Windows operation system and networks has been developed and programmed with Microsoft Visual C++ 6.0, Visual Basic 6.0 and SQL Server. The system can deal with patient's information throughout the anesthesia. It can collect and integrate the data from several kinds of medical equipment such as monitor, infusion pump and anesthesia machine automatically and real-time. After that, the system presents the anesthesia sheets automatically. The record system makes the anesthesia record more accurate and integral and can raise the anesthesiologist's working efficiency.

  15. Automated fiber pigtailing machine

    DOEpatents

    Strand, Oliver T.; Lowry, Mark E.

    1999-01-01

    The Automated Fiber Pigtailing Machine (AFPM) aligns and attaches optical fibers to optoelectonic (OE) devices such as laser diodes, photodiodes, and waveguide devices without operator intervention. The so-called pigtailing process is completed with sub-micron accuracies in less than 3 minutes. The AFPM operates unattended for one hour, is modular in design and is compatible with a mass production manufacturing environment. This machine can be used to build components which are used in military aircraft navigation systems, computer systems, communications systems and in the construction of diagnostics and experimental systems.

  16. Automated fiber pigtailing machine

    DOEpatents

    Strand, O.T.; Lowry, M.E.

    1999-01-05

    The Automated Fiber Pigtailing Machine (AFPM) aligns and attaches optical fibers to optoelectronic (OE) devices such as laser diodes, photodiodes, and waveguide devices without operator intervention. The so-called pigtailing process is completed with sub-micron accuracies in less than 3 minutes. The AFPM operates unattended for one hour, is modular in design and is compatible with a mass production manufacturing environment. This machine can be used to build components which are used in military aircraft navigation systems, computer systems, communications systems and in the construction of diagnostics and experimental systems. 26 figs.

  17. Automated wire preparation system

    NASA Astrophysics Data System (ADS)

    McCulley, Deborah J.

    The first step toward an automated wire harness facility for the aerospace industry has been taken by implementing the Wire Vektor 2000 into the wire harness preparation area. An overview of the Wire Vektor 2000 is given, including the facilities for wire cutting, marking, and transporting, for wire end processing, and for system control. Production integration in the Wire Vektor 2000 system is addressed, considering the hardware/software debug system and the system throughput. The manufacturing changes that have to be made in implementing the Wire Vektor 2000 are discussed.

  18. Automated Propellant Blending

    NASA Technical Reports Server (NTRS)

    Hohmann, Carl W. (Inventor); Harrington, Douglas W. (Inventor); Dutton, Maureen L. (Inventor); Tipton, Billy Charles, Jr. (Inventor); Bacak, James W. (Inventor); Salazar, Frank (Inventor)

    1999-01-01

    An automated propellant blending apparatus and method uses closely metered addition of countersolvent to a binder solution with propellant particles dispersed therein to precisely control binder precipitation and particle aggregation. A profile of binder precipitation versus countersolvent-solvent ratio is established empirically and used in a computer algorithm to establish countersolvent addition parameters near the cloud point for controlling the transition of properties of the binder during agglomeration and finishing of the propellant composition particles. The system is remotely operated by computer for safety, reliability and improved product properties, and also increases product output.

  19. Automated System Marketplace 1995: The Changing Face of Automation.

    ERIC Educational Resources Information Center

    Barry, Jeff; And Others

    1995-01-01

    Discusses trends in the automated system marketplace with specific attention to online vendors and their customers: academic, public, school, and special libraries. Presents vendor profiles; tables and charts on computer systems and sales; and sidebars that include a vendor source list and the differing views on procuring an automated library…

  20. [Genetics and genetic counseling].

    PubMed

    Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist.

  1. A transition from using multi-step procedures to a fully integrated system for performing extracorporeal photopheresis: A comparison of costs and efficiencies.

    PubMed

    Azar, Nabih; Leblond, Veronique; Ouzegdouh, Maya; Button, Paul

    2017-04-17

    The Pitié Salpêtrière Hospital Hemobiotherapy Department, Paris, France, has been providing extracorporeal photopheresis (ECP) since November 2011, and started using the Therakos(®) CELLEX(®) fully integrated system in 2012. This report summarizes our single-center experience of transitioning from the use of multi-step ECP procedures to the fully integrated ECP system, considering the capacity and cost implications. The total number of ECP procedures performed 2011-2015 was derived from department records. The time taken to complete a single ECP treatment using a multi-step technique and the fully integrated system at our department was assessed. Resource costs (2014€) were obtained for materials and calculated for personnel time required. Time-driven activity-based costing methods were applied to provide a cost comparison. The number of ECP treatments per year increased from 225 (2012) to 727 (2015). The single multi-step procedure took 270 min compared to 120 min for the fully integrated system. The total calculated per-session cost of performing ECP using the multi-step procedure was greater than with the CELLEX(®) system (€1,429.37 and €1,264.70 per treatment, respectively). For hospitals considering a transition from multi-step procedures to fully integrated methods for ECP where cost may be a barrier, time-driven activity-based costing should be utilized to gain a more comprehensive understanding the full benefit that such a transition offers. The example from our department confirmed that there were not just cost and time savings, but that the time efficiencies gained with CELLEX(®) allow for more patient treatments per year. © 2017 The Authors Journal of Clinical Apheresis Published by Wiley Periodicals, Inc.

  2. Evaluation of glycodendron and synthetically-modified dextran clearing agents for multi-step targeting of radioisotopes for molecular imaging and radioimmunotherapy

    PubMed Central

    Cheal, Sarah M.; Yoo, Barney; Boughdad, Sarah; Punzalan, Blesida; Yang, Guangbin; Dilhas, Anna; Torchon, Geralda; Pu, Jun; Axworthy, Don B.; Zanzonico, Pat; Ouerfelli, Ouathek; Larson, Steven M.

    2014-01-01

    A series of N-acetylgalactosamine-dendrons (NAG-dendrons) and dextrans bearing biotin moieties were compared for their ability to complex with and sequester circulating bispecific anti-tumor antibody (scFv4) streptavidin (SA) fusion protein (scFv4-SA) in vivo, to improve tumor to normal tissue concentration ratios for targeted radioimmunotherapy and diagnosis. Specifically, a total of five NAG-dendrons employing a common synthetic scaffold structure containing 4, 8, 16, or 32 carbohydrate residues and a single biotin moiety were prepared (NAGB), and for comparative purposes, a biotinylated-dextran with average molecular weight (MW) of 500 kD was synthesized from amino-dextran (DEXB). One of the NAGB compounds, CA16, has been investigated in humans; our aim was to determine if other NAGB analogs (e.g. CA8 or CA4) were bioequivalent to CA16 and/or better suited as MST reagents. In vivo studies included dynamic positron-emission tomography (PET) imaging of 124I-labelled-scFv4-SA clearance and dual-label biodistribution studies following multi-step targeting (MST) directed at subcutaneous (s.c.) human colon adenocarcinoma xenografts in mice. The MST protocol consists of three injections: first, a bispecific antibody specific for an anti-tumor associated glycoprotein (TAG-72) single chain genetically-fused with SA (scFv4-SA); second, CA16 or other clearing agent; and third, radiolabeled biotin. We observed using PET imaging of 124I-labelled-scFv4-SA clearance that the spatial arrangement of ligands conjugated to NAG (i.e. biotin) can impact the binding to antibody in circulation and subsequent liver uptake of the NAG-antibody complex. Also, NAGB CA32-LC or CA16-LC can be utilized during MST to achieve comparable tumor- to-blood ratios and absolute tumor uptake seen previously with CA16. Finally, DEXB was equally effective as NAGB CA32-LC at lowering scFv4-SA in circulation, but at the expense of reducing absolute tumor uptake of radiolabeled biotin. PMID:24219178

  3. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT ...

    EPA Pesticide Factsheets

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execution of the Soil Water Assessment Tool (SWAT) and KINEmatic Runoff and EROSion (KINEROS2) hydrologic models. The application of these two models allows AGWA to conduct hydrologic modeling and watershed assessments at multiple temporal and spatial scales. AGWA’s current outputs are runoff (volumes and peaks) and sediment yield, plus nitrogen and phosphorus with the SWAT model. AGWA uses commonly available GIS data layers to fully parameterize, execute, and visualize results from both models. Through an intuitive interface the user selects an outlet from which AGWA delineates and discretizes the watershed using a Digital Elevation Model (DEM) based on the individual model requirements. The watershed model elements are then intersected with soils and land cover data layers to derive the requisite model input parameters. The chosen model is then executed, and the results are imported back into AGWA for visualization. This allows managers to identify potential problem areas where additional monitoring can be undertaken or mitigation activities can be focused. AGWA also has tools to apply an array of best management practices. There are currently two versions of AGWA available; AGWA 1.5 for

  4. Space station advanced automation

    NASA Technical Reports Server (NTRS)

    Woods, Donald

    1990-01-01

    In the development of a safe, productive and maintainable space station, Automation and Robotics (A and R) has been identified as an enabling technology which will allow efficient operation at a reasonable cost. The Space Station Freedom's (SSF) systems are very complex, and interdependent. The usage of Advanced Automation (AA) will help restructure, and integrate system status so that station and ground personnel can operate more efficiently. To use AA technology for the augmentation of system management functions requires a development model which consists of well defined phases of: evaluation, development, integration, and maintenance. The evaluation phase will consider system management functions against traditional solutions, implementation techniques and requirements; the end result of this phase should be a well developed concept along with a feasibility analysis. In the development phase the AA system will be developed in accordance with a traditional Life Cycle Model (LCM) modified for Knowledge Based System (KBS) applications. A way by which both knowledge bases and reasoning techniques can be reused to control costs is explained. During the integration phase the KBS software must be integrated with conventional software, and verified and validated. The Verification and Validation (V and V) techniques applicable to these KBS are based on the ideas of consistency, minimal competency, and graph theory. The maintenance phase will be aided by having well designed and documented KBS software.

  5. Agile automated vision

    NASA Astrophysics Data System (ADS)

    Fandrich, Juergen; Schmitt, Lorenz A.

    1994-11-01

    The microelectronic industry is a protagonist in driving automated vision to new paradigms. Today semiconductor manufacturers use vision systems quite frequently in their fabs in the front-end process. In fact, the process depends on reliable image processing systems. In the back-end process, where ICs are assembled and packaged, today vision systems are only partly used. But in the next years automated vision will become compulsory for the back-end process as well. Vision will be fully integrated into every IC package production machine to increase yields and reduce costs. Modem high-speed material processing requires dedicated and efficient concepts in image processing. But the integration of various equipment in a production plant leads to unifying handling of data flow and interfaces. Only agile vision systems can act with these contradictions: fast, reliable, adaptable, scalable and comprehensive. A powerful hardware platform is a unneglectable requirement for the use of advanced and reliable, but unfortunately computing intensive image processing algorithms. The massively parallel SIMD hardware product LANTERN/VME supplies a powerful platform for existing and new functionality. LANTERN/VME is used with a new optical sensor for IC package lead inspection. This is done in 3D, including horizontal and coplanarity inspection. The appropriate software is designed for lead inspection, alignment and control tasks in IC package production and handling equipment, like Trim&Form, Tape&Reel and Pick&Place machines.

  6. Automated office blood pressure.

    PubMed

    Myers, Martin G; Godwin, Marshall

    2012-05-01

    Manual blood pressure (BP) is gradually disappearing from clinical practice with the mercury sphygmomanometer now considered to be an environmental hazard. Manual BP is also subject to measurement error on the part of the physician/nurse and patient-related anxiety which can result in poor quality BP measurements and office-induced (white coat) hypertension. Automated office (AO) BP with devices such as the BpTRU (BpTRU Medical Devices, Coquitlam, BC) has already replaced conventional manual BP in many primary care practices in Canada and has also attracted interest in other countries where research studies using AOBP have been undertaken. The basic principles of AOBP include multiple readings taken with a fully automated recorder with the patient resting alone in a quiet room. When these principles are followed, office-induced hypertension is eliminated and AOBP exhibits a much stronger correlation with the awake ambulatory BP as compared with routine manual BP measurements. Unlike routine manual BP, AOBP correlates as well with left ventricular mass as does the awake ambulatory BP. AOBP also simplifies the definition of hypertension in that the cut point for a normal AOBP (< 135/85 mm Hg) is the same as for the awake ambulatory BP and home BP. This article summarizes the currently available evidence supporting the use of AOBP in routine clinical practice and proposes an algorithm in which AOBP replaces manual BP for the diagnosis and management of hypertension.

  7. Maneuver Automation Software

    NASA Technical Reports Server (NTRS)

    Uffelman, Hal; Goodson, Troy; Pellegrin, Michael; Stavert, Lynn; Burk, Thomas; Beach, David; Signorelli, Joel; Jones, Jeremy; Hahn, Yungsun; Attiyah, Ahlam; hide

    2009-01-01

    The Maneuver Automation Software (MAS) automates the process of generating commands for maneuvers to keep the spacecraft of the Cassini-Huygens mission on a predetermined prime mission trajectory. Before MAS became available, a team of approximately 10 members had to work about two weeks to design, test, and implement each maneuver in a process that involved running many maneuver-related application programs and then serially handing off data products to other parts of the team. MAS enables a three-member team to design, test, and implement a maneuver in about one-half hour after Navigation has process-tracking data. MAS accepts more than 60 parameters and 22 files as input directly from users. MAS consists of Practical Extraction and Reporting Language (PERL) scripts that link, sequence, and execute the maneuver- related application programs: "Pushing a single button" on a graphical user interface causes MAS to run navigation programs that design a maneuver; programs that create sequences of commands to execute the maneuver on the spacecraft; and a program that generates predictions about maneuver performance and generates reports and other files that enable users to quickly review and verify the maneuver design. MAS can also generate presentation materials, initiate electronic command request forms, and archive all data products for future reference.

  8. Automating quantum experiment control

    NASA Astrophysics Data System (ADS)

    Stevens, Kelly E.; Amini, Jason M.; Doret, S. Charles; Mohler, Greg; Volin, Curtis; Harter, Alexa W.

    2017-03-01

    The field of quantum information processing is rapidly advancing. As the control of quantum systems approaches the level needed for useful computation, the physical hardware underlying the quantum systems is becoming increasingly complex. It is already becoming impractical to manually code control for the larger hardware implementations. In this chapter, we will employ an approach to the problem of system control that parallels compiler design for a classical computer. We will start with a candidate quantum computing technology, the surface electrode ion trap, and build a system instruction language which can be generated from a simple machine-independent programming language via compilation. We incorporate compile time generation of ion routing that separates the algorithm description from the physical geometry of the hardware. Extending this approach to automatic routing at run time allows for automated initialization of qubit number and placement and additionally allows for automated recovery after catastrophic events such as qubit loss. To show that these systems can handle real hardware, we present a simple demonstration system that routes two ions around a multi-zone ion trap and handles ion loss and ion placement. While we will mainly use examples from transport-based ion trap quantum computing, many of the issues and solutions are applicable to other architectures.

  9. A Demonstration of Automated DNA Sequencing.

    ERIC Educational Resources Information Center

    Latourelle, Sandra; Seidel-Rogol, Bonnie

    1998-01-01

    Details a simulation that employs a paper-and-pencil model to demonstrate the principles behind automated DNA sequencing. Discusses the advantages of automated sequencing as well as the chemistry of automated DNA sequencing. (DDR)

  10. Automated Power-Distribution System

    NASA Technical Reports Server (NTRS)

    Ashworth, Barry; Riedesel, Joel; Myers, Chris; Miller, William; Jones, Ellen F.; Freeman, Kenneth; Walsh, Richard; Walls, Bryan K.; Weeks, David J.; Bechtel, Robert T.

    1992-01-01

    Autonomous power-distribution system includes power-control equipment and automation equipment. System automatically schedules connection of power to loads and reconfigures itself when it detects fault. Potential terrestrial applications include optimization of consumption of power in homes, power supplies for autonomous land vehicles and vessels, and power supplies for automated industrial processes.

  11. Robotics/Automated Systems Technicians.

    ERIC Educational Resources Information Center

    Doty, Charles R.

    Major resources exist that can be used to develop or upgrade programs in community colleges and technical institutes that educate robotics/automated systems technicians. The first category of resources is Economic, Social, and Education Issues. The Office of Technology Assessment (OTA) report, "Automation and the Workplace," presents analyses of…

  12. Migration monitoring with automated technology

    Treesearch

    Rhonda L. Millikin

    2005-01-01

    Automated technology can supplement ground-based methods of migration monitoring by providing: (1) unbiased and automated sampling; (2) independent validation of current methods; (3) a larger sample area for landscape-level analysis of habitat selection for stopover, and (4) an opportunity to study flight behavior. In particular, radar-acoustic sensor fusion can...

  13. Robotics/Automated Systems Technicians.

    ERIC Educational Resources Information Center

    Doty, Charles R.

    Major resources exist that can be used to develop or upgrade programs in community colleges and technical institutes that educate robotics/automated systems technicians. The first category of resources is Economic, Social, and Education Issues. The Office of Technology Assessment (OTA) report, "Automation and the Workplace," presents analyses of…

  14. Automated Test-Form Generation

    ERIC Educational Resources Information Center

    van der Linden, Wim J.; Diao, Qi

    2011-01-01

    In automated test assembly (ATA), the methodology of mixed-integer programming is used to select test items from an item bank to meet the specifications for a desired test form and optimize its measurement accuracy. The same methodology can be used to automate the formatting of the set of selected items into the actual test form. Three different…

  15. Opening up Library Automation Software

    ERIC Educational Resources Information Center

    Breeding, Marshall

    2009-01-01

    Throughout the history of library automation, the author has seen a steady advancement toward more open systems. In the early days of library automation, when proprietary systems dominated, the need for standards was paramount since other means of inter-operability and data exchange weren't possible. Today's focus on Application Programming…

  16. Opening up Library Automation Software

    ERIC Educational Resources Information Center

    Breeding, Marshall

    2009-01-01

    Throughout the history of library automation, the author has seen a steady advancement toward more open systems. In the early days of library automation, when proprietary systems dominated, the need for standards was paramount since other means of inter-operability and data exchange weren't possible. Today's focus on Application Programming…

  17. Translation: Aids, Robots, and Automation.

    ERIC Educational Resources Information Center

    Andreyewsky, Alexander

    1981-01-01

    Examines electronic aids to translation both as ways to automate it and as an approach to solve problems resulting from shortage of qualified translators. Describes the limitations of robotic MT (Machine Translation) systems, viewing MAT (Machine-Aided Translation) as the only practical solution and the best vehicle for further automation. (MES)

  18. Automated Circulation. SPEC Kit 43.

    ERIC Educational Resources Information Center

    Association of Research Libraries, Washington, DC. Office of Management Studies.

    Of the 64 libraries responding to a 1978 Association of Research Libraries (ARL) survey, 37 indicated that they used automated circulation systems; half of these were commercial systems, and most were batch-process or combination batch process and online. Nearly all libraries without automated systems cited lack of funding as the reason for not…

  19. Classification of Automated Search Traffic

    NASA Astrophysics Data System (ADS)

    Buehrer, Greg; Stokes, Jack W.; Chellapilla, Kumar; Platt, John C.

    As web search providers seek to improve both relevance and response times, they are challenged by the ever-increasing tax of automated search query traffic. Third party systems interact with search engines for a variety of reasons, such as monitoring a web site’s rank, augmenting online games, or possibly to maliciously alter click-through rates. In this paper, we investigate automated traffic (sometimes referred to as bot traffic) in the query stream of a large search engine provider. We define automated traffic as any search query not generated by a human in real time. We first provide examples of different categories of query logs generated by automated means. We then develop many different features that distinguish between queries generated by people searching for information, and those generated by automated processes. We categorize these features into two classes, either an interpretation of the physical model of human interactions, or as behavioral patterns of automated interactions. Using the these detection features, we next classify the query stream using multiple binary classifiers. In addition, a multiclass classifier is then developed to identify subclasses of both normal and automated traffic. An active learning algorithm is used to suggest which user sessions to label to improve the accuracy of the multiclass classifier, while also seeking to discover new classes of automated traffic. Performance analysis are then provided. Finally, the multiclass classifier is used to predict the subclass distribution for the search query stream.

  20. Automated design of aerospace structures

    NASA Technical Reports Server (NTRS)

    Fulton, R. E.; Mccomb, H. G.

    1974-01-01

    The current state-of-the-art in structural analysis of aerospace vehicles is characterized, automated design technology is discussed, and an indication is given of the future direction of research in analysis and automated design. Representative computer programs for analysis typical of those in routine use in vehicle design activities are described, and results are shown for some selected analysis problems. Recent and planned advances in analysis capability are indicated. Techniques used to automate the more routine aspects of structural design are discussed, and some recently developed automated design computer programs are described. Finally, discussion is presented of early accomplishments in interdisciplinary automated design systems, and some indication of the future thrust of research in this field is given.